Alkynes and methods of reacting alkynes with 1,3-dipole-functional compounds

ABSTRACT

1,3-Dipole-functional compounds (e.g., azide functional compounds) can be reacted with certain alkynes in a cyclization reaction to form heterocyclic compounds. Useful alkynes (e.g., strained, cyclic alkynes) and methods of making such alkynes are also disclosed. The reaction of 1,3-dipole-functional compounds with alkynes can be used for a wide variety of applications including the immobilization of biomolecules on a substrate.

This application claims the benefit of U.S. Provisional Application Nos.61/004,021, filed Nov. 21, 2007; 61/007,674, filed Dec. 14, 2007; and61/137,061, filed Jul. 25, 2008, all of which are hereby incorporated byreference in their entireties.

GOVERNMENT FUNDING

The present invention was made with government support under a grantfrom the Research Resource Center for Biomedical Complex Carbohydratesof the National Institutes of Health (Grant No. P41—RR-5351). TheGovernment has certain rights in this invention.

BACKGROUND

Bioorthogonal reactions are reactions of materials with each other,wherein each material has limited or substantially no reactivity withfunctional groups found in vivo. The efficient reaction between an azideand a terminal alkyne, i.e., the most widely studied example of “click”chemistry, is known as a useful example of a bioorthogonal reaction. Inparticular, the Cu(I) catalyzed 1,3-dipolar cyclization of azides withterminal alkynes to give stable triazoles (e.g., Binder et al.,Macromol. Rapid Commun. 2008, 29:952-981) has been employed for tagginga variety of biomolecules including proteins, nucleic acids, lipids, andsaccharides. The cycloaddition has also been used for activity-basedprotein profiling, monitoring of enzyme activity, and the chemicalsynthesis of microarrays and small molecule libraries.

An attractive approach for installing azides into biomolecules is basedon metabolic labeling whereby an azide containing biosynthetic precursoris incorporated into biomolecules using the cells' biosyntheticmachinery. This approach has been employed for tagging proteins,glycans, and lipids of living systems with a variety of reactive probes.These probes can facilitate the mapping of saccharide-selectiveglycoproteins and identify glycosylation sites. Alkyne probes have alsobeen used for cell surface imaging of azide-modified bio-molecules and aparticularly attractive approach involves the generation of afluorescent probe from a non-fluorescent precursor by a [3+2]cycloaddition.

Despite the apparent utility of reacting an azide with a terminalalkyne, applications in biological systems using this reaction have beenpractically limited by factors including the undesirable presence of acopper catalyst. Thus, there is a continuing, unmet need for newbioorthogonal reactions.

SUMMARY

In one aspect, the present invention provides an alkyne, and methods ofmaking an alkyne. In one embodiment, the alkyne is of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³ and R⁴ independently representshydrogen or an organic group (e.g., which can include a cleavablelinker). Also provided are blends of certain alkynes with a polymer or acopolymer that can optionally form a copolymer micelle, which can beuseful, for example, for controlling the delivery of drugs as describedherein.

In another embodiment, the alkyne includes: a cleavable linker fragmentincluding at least two ends; an alkyne fragment attached to a first endof the cleavable linker fragment; and a biotinylated fragment attachedto a second end of the cleavable linker fragment. In preferredembodiments, the alkyne fragment includes a strained, cyclic alkynefragment. In certain embodiments, the alkyne further includes at leastone heavy mass isotope. Optionally, the alkyne further includes at leastone detectable label such as a fluorescent label.

Alkynes such as those described herein above can be reacted with atleast one 1,3-dipole-functional compound (e.g., an azide-functionalcompound, a nitrile oxide-functional compound, a nitrone-functionalcompound, an azoxy-functional compound, and/or an acyl diazo-functionalcompound) in a cyclization reaction to form a heterocyclic compound,preferably in the substantial absence of added catalyst (e.g., Cu(I)).Optionally, the reaction can take place within or on the surface of aliving cell. In certain embodiments, the at least one1,3-dipole-functional compound includes a 1,3-dipole-functionalbiomolecule such as a peptide, protein, glycoprotein, nucleic acid,lipid, saccharide, oligosaccharide, and/or polysaccharide. Optionally,the 1,3-dipole-functional biomolecule includes a detectable label suchas an affinity label. The heterocyclic compounds formed by the alkynewith the at least one 1,3-dipole-functional compound are also disclosedherein. In certain embodiments, the reaction between the alkyne and theat least one 1,3-dipole-functional compound can take place within or onthe surface of a living cell.

For embodiments in which the heterocyclic compound includes abiotinylated fragment, the heterocyclic compound can be bound to acompound that binds biotin, such as avidin and/or streptavidin.

In another aspect, the present invention provides a substrate having analkyne as described herein on the surface thereof. The substrate can bein the form of a resin, a gel, nanoparticles, or combinations thereof.Optionally, the substrate is a three-dimensional matrix. In preferredembodiments, the X group of an alkyne of Formula I represents a point ofattachment to the surface of the substrate. Such substrates can beuseful for immobilizing biomolecules such as peptides, proteins,glycoproteins, nucleic acids, lipids, saccharides, oligosaccharides,and/or polysaccharides. Articles including an immobilized biomolecule,such as a protein immobilized on a three-dimensional matrix, are alsodisclosed herein.

The compositions and methods disclosed herein can offer advantages overbioorthogonal reactions known in the art. See, for example, Baskin etal., QSAR Comb. Sci. 2007, 26:1211-1219. For example, alkynes of FormulaI as described herein (e.g., wherein X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³ and R⁴ independently representshydrogen or an organic group) surprisingly have been found to havehigher reactivity towards 1,3-dipole-functional compounds than otherstrained, cyclic alkynes (e.g., wherein X represents CH₂). See, forexample, Codelli, et al., J. Am. Chem. Soc. 2008, 130:11486-11493;Johnson et al., Chem. Commun. 2008, 3064-3066; Sletten et al., OrganicLetters 2008, 10:3097-3099; and Laughlin et al., Science 2008,320:664-667. Further, convenient methods having the flexibility toprepare a wide variety of alkynes of Formula I are disclosed herein. Inaddition, alkynes of Formula I have the capability of reacting not onlywith azides, but also a variety of other 1,3-dipole-functionalcompounds.

DEFINITIONS

The term “comprises” and variations thereof do not have a limitingmeaning where these terms appear in the description and claims.

As used herein, “a,” “an,” “the” “at least one,” and “one or more” areused interchangeably.

As used herein, the term “or” is generally employed in the sense asincluding “and/or” unless the context of the usage clearly indicatesotherwise.

Also herein, the recitations of numerical ranges by endpoints includeall numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2,2.75, 3, 3.80, 4, 5, etc.).

The above summary is not intended to describe each disclosed embodimentor every implementation of the present invention. The description thatfollows more particularly exemplifies illustrative embodiments. Inseveral places throughout the application, guidance is provided throughlists of examples, which examples can be used in various combinations.In each instance, the recited list serves only as a representative groupand should not be interpreted as an exclusive list.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates exemplary reagents for labeling azide-functionalbiomolecules.

FIG. 2 illustrates Scheme 1: exemplary reagents and conditions: a)TBSC1, pyridine; b) Br₂, CHCl₃; c) LDA, tetrahydrofuran; d)4-nitrophenyl chloroformate, pyridine, C₂Cl₂;e) N,N-dimethylformamide(DMF), triethylamine (TEA). LDA=lithium diisopropylamide,TBS=tert-butyldimethylsilyl.

FIG. 3 illustrates Scheme 2: exemplary reagents and conditions: a)compound 3 in methanol.

FIG. 4 illustrates exemplary metal-free cycloadditions of compound 3with azide-functional amino acid and saccharides.Boc=tert-butoxycarbonyl, TDS=thexyldimethylsilyl.

FIG. 5 illustrates Scheme 3: exemplary reaction conditions: a) 1,triethylamine, DMF, room temperature, 78%; b) 20% trifluoroacetic acid(TFA), room temperature, 95%; c)₂, TEA, DMF, room temperature, 68%.

FIG. 6 illustrates embodiments of cell-surface labeling with compounds 2and 9. Jurkat cells grown for three days in the absence or presence ofAc₄ManNAz (25 micromolar) were incubated a) with compounds 2 and 9 (30micromolar) for 0-180 minutes or b) with compounds 2 and 9 (0-100micromolar) for 1 hour at room temperature. Next, the cells wereincubated with avidin-FITC for 15 minutes at 4° C., after which celllysates were assessed for fluorescence intensity. Samples are indicatedas follows: blank cells incubated with 2 (◯) or 9 (□), and Ac,ManNAzcells incubated with 2 () or 9 (▪).

FIG. 7 illustrates an embodiment of toxicity assessment of cell labelingprocedure and cycloaddition reaction with compound 9. Jurkat cells grownfor 3 days in the absence (a) or presence (b) of Ac₄ManNAz (25micromolar) were incubated with compound 9 (0-100 micromolar) for 1 hourat room temperature. The cells were washed three times and thenincubated with avidin conjugated with fluorescein for 15 minutes at 4°C., after which cells were washed three times. Cell viability wasassessed at different points during the procedure with trypan blueexclusion; after incubation with 9 (black), after avidin-FITC incubation(grey), and after complete procedure (white). Treatment with Cu¹Cl (1mM) under the same conditions led to approximately 98% cell death forboth the blank and the Ac₄ManNAz treated cells.

FIG. 8 illustrates fluorescence images for embodiments of cells labeledwith compound 9 and avidin-Alexa Fluor 488. CHO cells grown for 3 daysin the absence (d-f) or presence (a-c) of Ac₄ManNAz (100 micromolar)were incubated with compound 9 (30 micromolar) for 1 hour at 4° C. (a,d) or room temperature (b, c, e, O, Next, cells were incubated withavidin-Alexa Fluor 488 for 15 minutes at 4° C. and, after washing,fixing, and staining for the nucleus with far-red-fluorescent dyeTO-PRO, imaged (a, b, d, e) or after washing incubated for 1 hour at 37°C. before fixing, nucleus staining, and imaging (c,f). Merged indicatesthat the images of cells labeled with Alexa Fluor (488 nanometers (nm))and TO-PRO-3 iodide (633 nm) are merged.

FIG. 9 illustrates exemplary compounds comprising an alkyne fragment, acleavable linker fragment, and a biotinylated fragment.

FIG. 10 illustrates Scheme 4: exemplary reaction conditions: a) DMF, 80°C., 70%; b) potassium thioacetate (KSAc), DMF, 60° C., 90%; c) NH₂NH₂,ethanol (EtOH), refluxing, 95%; d) N,N-diisopropylethylamine (DIPEA),DMF, 0° C., 56%; e) DIPEA, DMF, room temperature, 85%.

FIG. 11 illustrates Scheme 5: exemplary reaction conditions: a)p-toluenesulfonic acid (TsOH), room temperature, 81%; b) DMF, 80° C.,86%; c) 0.1N HCl, EtOH, room temperature, 90%; d) 9, NaH, DMF, 0° C.,88%; e) 0.1N HCl, EtOH, room temperature, 88%; f) CCl₄, PPh₃,dichloromethane (DCM), room temperature, 96%; g) KSAc, DMF, 60° C., 90%;h) NH₂NH₂, EtOH, refluxing, 95%; then (Boc)₂O, TEA, EtOH, 91%; i) 20%TFA, DCM, room temperature, 95%; j) DIPEA, DMF, 0° C.; then (Boc)₂O,TEA, EtOH, 60% over two steps; k) 20% TFA, DCM, room temperature, then 8DIPEA, DMF, room temperature, 80% over two steps.

FIG. 12 illustrates exemplary cleavable linkers.

FIG. 13 illustrates exemplary alkynes and a reactive diene.

FIG. 14 illustrates scheme 6: exemplary reaction conditions: a)TMSCH₂N₂, BF₃OEt₂, DCM, −10° C., 3 hours, 71%; b) NaBH₄, 1:1 EtOH/THF,room temperature, 7 hours, 100%; C) Br₂, CHCl₃, room temperature, 0.5hour, 58%; d) LDA, THF, 0.5 hour, 57%; e) Dess-Martin reagent, DCM, 0.5h; f) 4-nitrophenyl chloroformate, pyridine, DCM, 18 hours, 92%; g)tris(ethylene glycol)-1,8-diamine, TEA, DCM, room temperature, 3 hours,80%; h) bromoacetic acid, NaH, THF, 22%; i) tris(ethyleneglycol)-1,8-diamine, HATU coupling reagent, DIPEA, DMF, roomtemperature, 2 hours, 75%; j)N-{2-[2-(2-amino-ethoxy)-ethoxy]-ethyl}-2-aminooxy-acetamide, AcOH, 1:1DCM/MeOH, 63%.

FIG. 15 illustrates compounds 61-68 and second order constants.

FIG. 16 illustrates scheme 7: exemplary reagents and conditions: a)LiAlH₄, AlCl₃, Et₂O, 0° C., 61%; b) Br₂, CHCl₃, 0° C., 58%; c) potassiumt-butoxide (t-BuOK), THF, room temperature, 25%.

FIG. 17 illsuprates scheme 8: exemplary reagents and conditions: a) TEA,CH₂Cl₂, room temperature, 77%.

FIG. 18 illustrates scheme 9: exemplary reagents and conditions: a) NaH,benzyl bromide, DMF, room temperature, 59%; b) acetic anhydride (Ac₂O),pyridine, room temperature, 81%.

FIG. 19 illustrates scheme 10: exemplary reagents and conditions: a)LDA, Et₃SiCl, THF, room temperature, 85%; b) SELECTFLUOR fluorinatingreagent, DMF, room temperature, 66% c) LDA, Et₃SiCl, THF, roomtemperature, 79%; d) SELECTFLUOR fluorinating reagent, DMF, roomtemperature, 51%; e) NaBH₄, EtOH, room temperature, 78%; f) Br₂, CHCl₃,0° C., 46%; g) c) t-BuOK, THF, room temperature, 49%.

FIG. 20 illustrates the use of copolymer micelles for drug delivery. A)Polyester and polyethyleneglycol groups self-assembled in water. B)Functionalized copolymer micelles as drug delivery devices. C)Oxime-modified alkyne derivatives of copolymer micelles.

FIG. 21 illustrates the preparation of macromolecules with4-dibenzocyclooctyne functionality.

FIG. 22 illustrates cycloadditions of 4-dibenzocyclooctynol with variousnitrones. Compounds were mixed at 1:1 molar ratio at a finalconcentration of 6 mM and reacted for a time indicated.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Alkynes such as those described herein can be reacted with at least one1,3-dipole-functional compound in a cyclization reaction to form aheterocyclic compound. In preferred embodiments, the reaction can becarried out in the substantial absence of added catalyst (e.g., Cu(I)).Exemplary 1,3-dipole-functional compounds include, but are not limitedto, azide-functional compounds, nitrile oxide-functional compounds,nitrone-functional compounds, azoxy-functional compounds, and/or acyldiazo-functional compounds.

Exemplary alkynes include alkynes of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group (and preferably a C1-C10 organic moiety); each R²is independently selected from the group consisting of hydrogen,halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and a C1-C10organic group (and preferably a C1-C10 organic moiety); X representsC═O, C═N—OR³, C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³ and R⁴independently represents hydrogen or an organic group (and in someembodiments an organic moiety). In preferred embodiments, each R¹represents hydrogen and/or each R² represents hydrogen. Optionally, R³includes a covalently bound organic dye (e.g., a fluorescent dye).

As used herein, the term “organic group” is used for the purpose of thisinvention to mean a hydrocarbon group that is classified as an aliphaticgroup, cyclic group, or combination of aliphatic and cyclic groups(e.g., alkaryl and aralkyl groups). In the context of the presentinvention, suitable organic groups for compounds of this invention arethose that do not interfere with the reaction of an alkyne with a1,3-dipole-functional compound to form a heterocyclic compound. In thecontext of the present invention, the term “aliphatic group” means asaturated or unsaturated linear or branched hydrocarbon group. This termis used to encompass alkyl, alkenyl, and alkynyl groups, for example.The term “alkyl group” means a saturated linear or branched monovalenthydrocarbon group including, for example, methyl, ethyl, n-propyl,isopropyl, text-butyl, amyl, heptyl, and the like. The term “alkenylgroup” means an unsaturated, linear or branched monovalent hydrocarbongroup with one or more olefinically unsaturated groups (i.e.,carbon-carbon double bonds), such as a vinyl group. The term “alkynylgroup” means an unsaturated, linear or branched monovalent hydrocarbongroup with one or more carbon-carbon triple bonds. The term “cyclicgroup” means a closed ring hydrocarbon group that is classified as analicyclic group, aromatic group, or heterocyclic group. The term“alicyclic group” means a cyclic hydrocarbon group having propertiesresembling those of aliphatic groups. The term “aromatic group” or “arylgroup” means a mono- or polynuclear aromatic hydrocarbon group. The term“heterocyclic group” means a closed ring hydrocarbon in which one ormore of the atoms in the ring is an element other than carbon (e.g.,nitrogen, oxygen, sulfur, etc.).

As a means of simplifying the discussion and the recitation of certainterminology used throughout this application, the teens “group” and“moiety” are used to differentiate between chemical species that allowfor substitution or that may be substituted and those that do not soallow for substitution or may not be so substituted. Thus, when the term“group” is used to describe a chemical substituent, the describedchemical material includes the unsubstituted group and that group withnonperoxidic O, N, S, Si, or F atoms, for example, in the chain as wellas carbonyl groups or other conventional substituents. Where the term“moiety” is used to describe a chemical compound or substituent, only anunsubstituted chemical material is intended to be included. For example,the phrase “alkyl group” is intended to include not only pure open chainsaturated hydrocarbon alkyl substituents, such as methyl, ethyl, propyl,tert-butyl, and the like, but also alkyl substituents bearing furthersubstituents known in the art, such as hydroxy, alkoxy, alkylsulfonyl,halogen atoms, cyano, nitro, amino, carboxyl, etc. Thus, “alkyl group”includes ether groups, haloalkyls, nitroalkyls, carboxyalkyls,hydroxyalkyls, sulfoalkyls, etc. On the other hand, the phrase “alkylmoiety” is limited to the inclusion of only pure open chain saturatedhydrocarbon alkyl substituents, such as methyl, ethyl, propyl,tert-butyl, and the like.

Alkynes of Formula I are typically strained, cyclic alkynes.Surprisingly it has been found that alkynes of Formula I as describedherein (e.g., wherein X represents C═O, C═N—OR³, C═N—NR³R⁴, CHOR³, orCHNHR³; and each R³ and R⁴ independently represents hydrogen or anorganic group) have been found to have higher reactivity towards1,3-dipole-functional compounds than other strained, cyclic alkynes(e.g., wherein X represents CH₂).

In certain embodiments of alkynes of Formula I, X can represent C═N—OR³wherein R³ is an organic group. For example, R³ can have the formula—(CH₂)_(a)C(O)Y, wherein: a is 1-3; Y represents OH or NHR⁵; and R⁵represents hydrogen or a biotinylation product of a primaryamine-containing organic group. The primary amine-containing group can,for example, be of the formula—(CH₂CH₂O)_(b)(CH₂)_(c)-L_(d)-(CH₂CH₂O)_(e)(CH₂)_(f)NH₂ and/or—(CD₂CD₂O)_(b)(CD₂)_(c)-L_(d)-(CD₂CD₂O)_(e)(CD₂)_(f)NH₂, wherein b=0 to100 (e.g., 10 to 100); c=0 to 100 (and preferably 1 to 10); d=0 to 100(and preferably 1 to 10); e=0 to 100 (e.g., 10 to 100); f=0 to 100 (andpreferably 1 to 10); and L is an optional cleavable linker (e.g., adisulfide).

In certain embodiments of alkynes of Formula I, X can represent CHOR³,wherein R³ is selected from the group consisting of an alkyl group, anaryl group, an alkaryl group, and an aralkyl group. For example, R³ canhave the formula —C(O)Z, wherein: Z represents an alkyl group, OR⁶, orNHR⁷; and R⁶ and R⁷ are each independently selected from the groupconsisting of an alkyl group, an aryl group, an alkaryl group, and anaralkyl group. In certain embodiments, R⁷ can be a biotinylation productof a primary amine-containing organic group. The primaryamine-containing group can, for example, be of the formula—(CF₂CH₂O)_(b)(CH₂)_(c)-L_(d)-(CF₂CH₂O)_(e)(CH₂)_(f)NH₂ and/or—(CD₂CD₂O)_(b)(CD₂)_(c)-L_(d)-(CD2CD₂O)_(e)(CD₂)_(f)NR₂, wherein b=0 to100 (e.g., 10 to 100); c=0 to 100 (and preferably 1 to 10); d=0 to 100(and preferably 1 to 10); e=0 to 100 (e.g., 10 to 100); f=0 to 100 (andpreferably 1 to 10); and L is an optional cleavable linker (e.g., adisulfide).

An exemplary alkyne of Formula I is the species in which X representsC═O, an alkyne of the formula:

Another exemplary alkyne of Formula I is the species in which Xrepresents CHOH, an alkyne of the formula:

Another exemplary alkyne of Formula I is the species in which Xrepresents CHNH₂, an alkyne of the formula:

Another exemplary alkyne of Formula I is the species in which Xrepresents C═N—OR³, an alkyne of the formula:

wherein R³ represents hydrogen or an organic group (and in someembodiments an organic moiety).

Additional exemplary alkynes include alkynes that have: a cleavablelinker fragment including at least two ends; an alkyne fragment attachedto a first end of the cleavable linker fragment; and a biotinylatedfragment attached to a second end of the cleavable linker fragment. Incertain embodiments, the alkyne fragment includes a strained, cyclicalkyne fragment. In certain embodiments, the alkyne further includes atleast one heavy mass isotope. Optionally, the alkyne further includes atleast one detectable label (e.g., a fluorescent label).

In certain embodiments of alkynes of Formula I, X can represent apolymeric or a copolymeric group. For embodiments in which X representsa copolymeric group, the copolymeric group can include a hydrophilicsegment and a hydrophobic segment. For example, the copolymeric groupcan include a fragment of the formula-[CH₂CH₂O]_(n)—[C(O)(CH₂)₅O]_(m)—H,wherein n=0 to 100 (e.g., 10 to 100) and m=0 to 100 (e.g., 10 to 100).Surfaces on which drops of water or aqueous solutions exhibit a contactangle of less than 90 degrees are commonly referred to as “hydrophilic.”The contact angle of a hydrophobic material with water is typicallygreater than 90 degrees.

Exemplary methods of making alkynes of Formula I are also disclosedherein. In one embodiment, the method includes: brominating an alkene ofthe formula:

to provide a dibromide of the formula:

and dehydrobrominating the dibromide of Formula XV to provide the alkyneof the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³ and R⁴ independently representshydrogen or an organic group (e.g., which can include a cleavablelinker). A wide variety of 1,3-dipole-functional compounds can be usedto react with the alkynes disclosed herein. As used herein, a“1,3-dipole-functional compound” is meant to include compounds having atleast one 1,3-dipole group attached thereto. As used herein, a“1,3-dipole group” is intended to refer to a group having a three-atompi-electron system containing 4 electrons delocalized over the threeatoms. Exemplary 1,3-dipole groups include, but are not limited to,azides, nitrile oxides, nitrones, azoxy groups, and acyl diazo groups.In certain embodiments, the 1,3-dipole-functional compound can be abiomolecule having at least one 1,3-dipole group attached thereto.Optionally, the at least one 1,3-dipole-functional compound can includea detectable label (e.g., an immunoassay or affinity label).

One or more 1,3-dipole-functional compounds (e.g., azide-functionalcompounds, nitrile oxide-functional compounds, nitrone-functionalcompounds, azoxy-functional compounds, and/or acyl diazo-functionalcompounds) can be combined with an alkyne as described herein underconditions effective to react in a cyclization reaction and form aheterocyclic compound. Preferably, conditions effective to form theheterocyclic compound can include the substantial absence of addedcatalyst. Conditions effective to form the heterocyclic compound canalso include the presence or absence of a wide variety of solventsincluding, but not limited to, aqueous (e.g., water) and non-aqueoussolvents; protic and aprotic solvents; polar and non-polar solvents; andcombinations thereof. The heterocyclic compound can be formed over awide temperature range, with a temperature range of 0° C. to 40° C. (andin some embodiments 23° C. to 37° C.) being particularly useful whenbiomolecules are involved. Conveniently, reaction times can be less thanone day, and sometimes one hour or even less.

In certain embodiments, the cyclization reaction between the one or more1,3-dipole-functional compounds and the alkyne can take place within oron the surface of a living cell. Such reactions can take place in vivoor ex vivo. As used herein, the term “in vivo” refers to a reaction thatis within the body of a subject. As used herein, the term “ex vivo”refers to a reaction in tissue (e.g., cells) that has been removed, forexample, isolated, from the body of a subject. Tissue that can beremoved includes, for example, primary cells (e.g., cells that haverecently been removed from a subject and are capable of limited growthor maintenance in tissue culture medium), cultured cells (e.g., cellsthat are capable of extended growth or maintenance in tissue culturemedium), and combinations thereof.

An exemplary embodiment of a 1,3-dipole-functional compound is anazide-functional compound of the formula R⁸—N₃ (e.g., represented by thevalence structure R⁸—N—N═N⁺), wherein R⁸ represents and organic group(e.g., a biomolecule). Optionally, R⁸ can include a detectable label(e.g., an affinity label).

The cyclization reaction of an azide-functional compound of the formulaR⁸—N₃ with an exemplary alkyne of Formula I can result in one or moreheterocyclic compounds of the formulas:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; each R³ and R⁴ independently representshydrogen or an organic group (e.g., which can include a cleavablelinker); and R⁸ represents an organic group (e.g., which can include abiomolecule and optionally a cleavable linker).

Another exemplary embodiment of a 1,3-dipole-functional compound is anitrile oxide-functional compound of the formula R⁸—CNO (e.g.,represented by the valence structure R⁸—⁺C═N—O⁻), wherein R⁸ representsand organic group (e.g., a biomolecule). Optionally, R⁸ can include adetectable label (e.g., an affinity label).

The cyclization reaction of a nitrile oxide-functional compound of theformula R⁸—CNO with an exemplary alkyne of Formula I can result in oneor more heterocyclic compounds of the formulas:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; each R³ and R⁴ independently representshydrogen or an organic group (e.g., which can include a cleavablelinker); and R⁸ represents an organic group (e.g., which can include abiomolecule and optionally a cleavable linker).

Another exemplary embodiment of a 1,3-dipole-functional compound is anitrone-functional compound of the formula (R¹⁰)₂CN(R¹⁰)O (e.g.,represented by the valence structure (R¹⁰)₂C=⁺N(R¹⁰)—O⁻) wherein eachR¹⁰ independently represents hydrogen or an organic group, with theproviso that at least one R¹⁰ represents an organic group (e.g., abiomolecule). Optionally, at least one R¹⁰ can include a detectablelabel (e.g., an affinity label).

The cyclization reaction of a nitrone-functional compound of the formula(R¹⁰)₂CN(R¹⁰)O with an exemplary alkyne of Formula I can result in oneor more heterocyclic compounds of the formulas:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³, R⁴, and R¹⁰ independentlyrepresents hydrogen or an organic group, with the proviso that at leastone R¹⁰ represents an organic group (e.g., which can include abiomolecule and optionally a cleavable linker).

Another exemplary embodiment of a 1,3-dipole-functional compound is anazoxy-functional compound of the formula R¹⁰−N═⁺N(R¹⁰)—O⁻)(e.g.,represented by the valence structure R¹⁰−N=⁺N(R¹⁰)−O⁻, wherein each R¹⁰independently represents hydrogen or an organic group, with the provisothat at least one R¹⁰ represents an organic group (e.g., a biomolecule).Optionally, at least one R¹⁰ can include a detectable label (e.g., anaffinity label).

The cyclization reaction of an azoxy-functional compound of the formulaR¹⁰—NN(R¹⁰)O with an exemplary alkyne of Formula I can result in one ormore heterocyclic compounds of the formulas:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³, R⁴, and R¹⁰ independentlyrepresents hydrogen or an organic group, with the proviso that at leastone R¹⁰ represents an organic group (e.g., which can include abiomolecule and optionally a cleavable linker).

For embodiments in which the heterocyclic compound formed from thecyclization reaction between the alkyne and the one or more1,3-dipole-functional compounds includes a detectable label, theheterocyclic compound can be detected using the detectable label. Forexample, for embodiments in which the detectable label is an affinitylabel, affinity binding (e.g., affinity chromatography) can be used todetect the heterocyclic compound.

In addition, for embodiments in which the heterocyclic compound formedfrom the cyclization reaction between the alkyne and the one or more1,3-dipole-functional compounds includes a biotinylated fragment, theheterocyclic compound can be bound by contacting the heterocycliccompound with a compound that binds biotin (e.g., avidin and/orstreptavidin). Further, the bound heterocyclic compound can be detectedby methods described herein.

Cyclization reactions between alkynes as disclosed herein and1,3-dipole-functional compounds can be used for a wide variety ofapplications. For example, an alkyne as disclosed herein can be attachedto the surface of a substrate. In certain embodiments, the X group ofthe alkyne represents a point of attachment to the surface of thesubstrate. One of skill in the art will recognize that the X group canadvantageously be selected to include functionality (e.g., biotin,activated esters, activated carbonates, and the like) to enableattachment of the alkyne to a functional substrate (e.g., aminefunctionality, thiol functionality, and the like) through a wide varietyof reactions.

Substrates having an alkyne attached to the surface thereof can bereacted with 1,3-dipole-functional compounds to form heterocycliccompounds, effectively chemically bonding the 1,3-dipole-functionalcompounds to the substrate. Such substrates can be, for example, in theform of resins, gels, nanoparticles (e.g., including magneticnanoparticles), or combinations thereof. In certain embodiments, suchsubstrates can be in the form of microarrays or even three-dimensionalmatrices or scaffolds. Exemplary three-dimensional matrices include, butare not limited to, those available under the trade designationsALGIMATRIX 3D Culture system, GELTRIX matrix, and GIBCOthree-dimensional scaffolds, all available from Invitrogen (Carlsbad,Calif.). Such three-dimensional matrices can be particularly useful forapplications including cell cultures.

1,3-Dipole-functional biomolecules (e.g., 1,3-dipole-functionalpeptides, proteins, glycoproteins, nucleic acids, lipids, saccharides,oligosaccharides, and/or polysaccharides) can be immobilized on, andpreferably covalently attached to, a substrate surface by contacting the1,3-dipole-functional biomolecules with a substrate having an alkyneattached to the surface thereof under conditions effective for acyclization reaction to form a heterocyclic compound. Preferably,conditions effective to form the heterocyclic compound can include thesubstantial absence of added catalyst. Conditions effective to form theheterocyclic compound can also include the presence or absence of a widevariety of solvents including, but not limited to, aqueous (e.g., waterand other biological fluids) and non-aqueous solvents; protic andaprotic solvents; polar and non-polar solvents; and combinationsthereof. The heterocyclic compound can be formed over a wide temperaturerange, with a temperature range of 0° C. to 40° C. (and in someembodiments 23° C. to 37° C.) being particularly useful. Conveniently,reaction times can be less than one day, and sometimes one hour or evenless.

For example, when the substrate is in the form of a three-dimensionalmatrix and the 1,3-dipole-functional biomolecule is a1,3-dipole-functional protein (e.g., an azide-functional protein), thecyclization reaction can result in an article having a proteinimmobilized on a three-dimensional matrix. Such matrices can have a widevariety of uses including, but not limited to, separating and/orimmobilizing cell lines. Particularly useful proteins for theseapplications include, but are not limited to, collagen, fibronectin,gelatin, laminin, vitronectin, and/or other proteins commonly used forcell plating.

For another example, cyclization reactions between 1,3-dipole-functionalcompounds and alkynes of Formula I in which X represents a polymeric ora copolymeric group can be used, for example, for controlling thedelivery of drugs as described herein below. For example, alkynes ofFormula I in which X represents a copolymeric group including ahydrophilic segment and a hydrophobic segment can be blended with apolymer or a copolymer. Further, when an alkyne of Formula I in which Xrepresents a copolymeric group including a hydrophilic segment and ahydrophobic segment is blended with a copolymer having a hydrophilicsegment and a hydrophobic segment, a copolymer micelle can be formed.Particularly useful copolymers having a hydrophilic segment and ahydrophobic segment include those of the formulaR⁹O—[CH₂CH₂O]_(p)—[C(O)(CH₂)₅O]₀—H, wherein R⁹ represents an alkyl group(e.g., methyl), p=0 to 100 (e.g., 1 to 100), and o=0 to 100 (e.g., 1 to100).

The copolymer micelles that include an alkyne of Formula I as describedherein above can advantageously be used to control the delivery ofdrugs. For example, a copolymer micelle that includes an alkyne ofFormula I can be combined with at least one 1,3-dipole-functional drugand allowed to react under conditions effective to form a heterocycliccompound and attach the drug to the copolymer micelle. See, for example,Nishiyama et al., Adv. Polym. Sci. 2006, 193:67-101; Gaucher et al., J.Control. Release 2005, 109:169-188; Choi et al., J. Dispersion Sci.Tech. 2003, 24:475-487; Lavasanifar et al., Adv. Drug Delivery Rev.2002, 54:169-190; and Rosier et al., Adv. Drug Delivery Rev. 2001,53:95-108.

Further, because it does not require a toxic catalyst such as copper,the novel cycloaddition reaction provided by the invention can be usedfor labeling of living cells. For example, cells can first bemetabolically labeled with an azide-functional precursor to produceazide-functional biomolecules (also referred to as bioconjugates) suchas azide-functional glycoproteins (also referred to as glycoconjugates).The cells can then be contacted with an alkyne of Formula I, either insolution or on a substrate as discussed above, under conditions topermit labeling (via the cycloaddition reaction) of the azide-functionalbiomolecules at the surface of the cell. The resulting triazoleconjugate can be detected at the cell surface, or it can be endocytosedby the cell and detected inside the cell.

Alkynes of Formula I can also have utility for imaging applicationsincluding, for example, as reagents for magnetic resonance imaging(MRI). For another example, alkynes of Formula I can contain afluorescent tag. Alkynes of Formula I can also be useful in qualitativeor quantitative proteomics and glycomics applications utilizing massspectrometry. The alkyne of Formula I can be selected to contain one ormore heavy mass isotopes, such as deuterium, ¹³C, ¹⁵N, ³⁵S and the like,and then can be used to label and/or immobilize azide-functionalbiomolecules as described herein.

Alkynes of Formula I can also have utility for applications such asvaccines. For example, alkynes of Formula I can be reacted with anazide-functional protein (e.g., an azide-functional carbohydrate, anazide-functional peptide, and/or an azide-functional glycopeptide), andthe resulting triazole conjugate can be used as a carrier protein forthe vaccine.

The present invention is illustrated by the following examples. It is tobe understood that the particular examples, materials, amounts, andprocedures are to be interpreted broadly in accordance with the scopeand spirit of the invention as set forth herein.

EXAMPLES Example 1 Visualizing Metabolically Labeled Glycoconjugates ofLiving Cells by Copper-Free and Fast Huisgen Cycloadditions

Azides, which are extremely rare in biological systems, are emerging asattractive chemical handles for bioconjugation (Kolb and Sharpless, DrugDiscovery Today 2003, 8:1128-1137; Dedola et al., Org. Biomol. Chem.2007 5:1006-1017; Moses and Moorhouse, Chem. Soc. Rev. 2007,36:1249-1262; Nandivada et al., Adv. Mater. 2007, 19:2197-2208; Wu andFokin, Aldrichimica Acta 2007, 40:7-17). In particular, theCu¹-catalyzed 1,3-dipolar cycloaddition of azides with terminal alkynesto give stable triazoles (Rostovtsev et al., Angew. Chem. 2002,114:2708-2711; Rostovtsev et al., Angew. Chem. Int. Ed. 2002,41:2596-2599; Tornoe et al., I Org. Chem. 2002, 67:3057-3064) has beenemployed for the tagging of a variety of biomolecules, (Chin et al.,Science 2003, 301:964-967; Wang et al., J. Am. Chem. Soc. 2003,125:3192-3193; Kho et al., Proc. Natl. Acad. Sci. USA 2004,101:12479-12484; Gierlich et al., Org. Lett. 2006, 8:3639-3642; Link etal., Proc. Natl. Acad. Sci. USA 2006, 103:10180-10185) activity-basedprotein profiling (Speers et al., J. Am. Chem. Soc. 2003,125:4686-4687), and the chemical synthesis of microarrays andsmall-molecule libraries (Sun et al., Bioconjugate Chem. 2006,17:52-57).

An attractive approach for installing azides into biomolecules is basedon metabolic labeling, whereby an azide-containing biosyntheticprecursor is incorporated into biomolecules by using the cells'biosynthetic machinery (Prescher and Bertozzi, Nat. Chem. Biol. 2005,1:13-21). This approach has been employed for tagging proteins, glycans,and lipids of living systems with a variety of reactive probes. Theseprobes can facilitate the mapping of saccharide-selective glycoproteinsand identify glycosylation sites (Hanson et al., J. Am. Chem. Soc. 2007,129:7266-7267). Alkyne probes have also been used for cell-surfaceimaging of azide-modified biomolecules, and a particularly attractiveapproach involves the generation of a fluorescent probe from anonfluorescent precursor by a [3+2] cycloaddition (Sivakumar et al.,Org. Lett. 2004, 6:4603-4606).

The cellular toxicity of the Cu¹ catalyst has precluded applicationswherein cells must remain viable (Link and Tinel, J. Am. Chem. Soc.2003, 125:11164-11165), and hence there is a great need for thedevelopment of Cu¹-free [3+2] cycloadditions (Turner et al., J. Am.Chem. Soc. 1973, 95:790-792; Agard et al., J. Am. Chem. Soc. 2004,126:15046-15047; vanBerkel et al., Chem-BioChem 2007, 8:1504-1508). Inthis respect, alkynes can be activated by ring strain, and, for example,constraining an alkyne within an eight-membered ring creates 18kcalmol⁻¹ of strain, much of which is released in the transition stateupon [3+2] cycloaddition with an azide (Turner et al., J. Am. Chem. Soc.1973, 95:790-792; Agard et al., J. Am. Chem. Soc. 2004,126:15046-15047). As a result, cyclooctynes such as 1 react with azidesat room temperature without the need for a catalyst (FIG. 1). Thestrain-promoted cycloaddition has been used to label biomoleculeswithout observable cytotoxicity (Agard et al., J. Am. Chem. Soc. 2004,126:15046-15047). The scope of the approach has, however, been limitedbecause of the slow rate of reaction (Agard et al., ACS Chem. Biol.2006, 1:644-648). Appending electron-withdrawing groups to the octynering can increase the rate of strain-promoted cycloadditions; however,currently Staudinger ligation with phosphine 2 offers the mostattractive reagent for cell-surface labeling with azides.

It was envisaged that 4-dibenzocyclooctynols such as compound 3 would beideal for labeling living cells with azides because the aromatic ringsare expected to impose additional ring strain and conjugate with thealkyne, thereby increasing the reactivity of the alkyne in metal-free[2+3] cycloadditions with azides. The compound should, however, haveexcellent stability because the ortho hydrogen atoms of the aromaticrings shield the alkyne from nucleophilic attack. Furthermore, thehydroxy group of 3 provides a handle for the incorporation of tags suchas fluorescent probes and biotin.

Compound 3 could be prepared easily from known (Jung et al., J. Org.Chem. 1978, 43:3698-3701; Jung and Miller, J. Am. Chem. Soc. 1981,103:1984-1992) 3-hydroxy-1,2:5,6-dibenzocycloocta-1,5,7-triene (4) byprotection of the hydroxy group as a TBS ether to give 5, which wasbrominated to provide dibromide 6 in a yield of 60% (Scheme 1; FIG. 2).The TBS protecting group was lost during the latter transformation, butthe bromination was low yielding when performed on alcohol 4.Dehydrobromination of 6 by treatment with LDA in THF at 0° C. (Seitz etal., Angew. Chem. 1969, 81:427-428; Seitz et al., Angew. Chem. Int. Ed.Engl. 1969, 8:447-448) gave the target cyclooctyne 3 in a yield of 45%.

Compound 3 has an excellent, long shelf life and after treatment did notreact with nucleophiles such as thiols and amines. However, uponexposure to azides a fast reaction took place and gave the correspondingtriazoles in high yield. For example, triazoles 10-13 were obtained inquantitative yields as mixtures of regioisomers by reaction of thecorresponding azido-containing sugar and amino acid derivatives with 3in methanol for 30 minutes (Scheme 2; FIG. 3 and FIG. 4). The progressof the reaction of 3 with benzyl azide in methanol and in a mixture ofwater/acetonitrile (1:4 v/v) was monitored by ¹H NMR spectroscopy byintegration of the benzylic proton signals, and second-order rateconstants of 0.17 and 2.3 m⁻¹ s⁻¹ respectively, were determined. Therate constant of the reaction with 3 in acetonitrile/water isapproximately three orders of magnitude greater than that withcyclooctyne 1.

Having established the superior reactivity of 3, we focused ourattention on the preparation of a derivative of 4-dibenzocyclooctynol(9; Scheme 1; FIG. 2), which is modified with biotin. Such a reagentshould make it possible to visualize biomolecules after metabolicallylabeling cells with an azido-containing biosynthetic precursor, followedby cycloaddition with 9 and treatment with avidin modified with afluorescence probe. Alternatively, biotinylation of glycoconjugates with9 should make it possible to isolate these derivatives for glycocomicsstudies using avidin immobilized on a solid support. Compound 9 couldeasily be prepared by a two-step reaction involving treatment of 3 with4-nitrophenyl chloroformate to give activated intermediate 7, followedby immediate reaction with 8. 4-dibenzocyclooctynol (9) may also befunctionalized with a fluorescent tag to yield a fluorescent derivative(Scheme 3; FIG. 5).

Next, Jurkat cells were cultured in the presence of 25 micromolarN-azidoacetylmannosamine (Ac₄ManNAz) for three days to metabolicallyintroduce N-azidoacetylsialic acid (SiaNAz) moieties into glycoproteins(Luchansky and Bertozzi, Chem-BioChem 2004, 5:1706-1709). As a negativecontrol, Jurkat cells were employed that were grown in the absence ofAc₄ManNAz. The cells were exposed to a 30 micromolar solution ofcompound 9 for various time periods, and after washing, the cells werestained with avidin-fluorescein isothiocyanate (FITC) for 15 minutes at4° C. The efficiency of the two-step cell-surface labeling wasdetermined by measuring the fluorescence intensity of the cell lysates.For comparison, the cell-surface azido moieties were also labeled byStaudinger ligation with biotin-modified phosphine 2 followed bytreatment with avidin-FITC. The labeling with 9 was almost completeafter an incubation time of 60 minutes (FIG. 6 a).

Interestingly, under identical conditions phosphine 2 (Agard et al., ACSChem. Biol. 2006, 1:644-648) gave significantly lower fluorescentintensities, indicating that cell surface labeling by Staudingerligation is slower and less efficient. In each case, the control cellsexhibited very low fluorescence intensities, demonstrating thatbackground labeling is negligible. It was found that the two-steplabeling approach with 9 had no effect on cell viability, as determinedby morphology and exclusion of trypan blue (data not shown; FIG. 7).

The concentration dependence of the cell-surface labeling was studied byincubation of cells with various concentrations of 2 and 9 followed bystaining with avidin-FTIC (FIG. 6 b). As expected, cells displayingazido moieties showed a dose-dependent increase in fluorescenceintensity. Reliable fluorescent labeling was achieved at a 3 micromolarconcentration of 9; however, optimal results were obtained atconcentrations ranging from 30 to 100 micromolar. No increase inlabeling was observed at concentrations higher than 100 micromolar owingto the limited solubility of 9.

Next, attention was focused on visualizing azido-containingglycoconjugates of living cells by confocal microscopy. Thus, adherentChinese hamster ovary (CHO) cells were cultured in the presence ofAc₄ManNAz (100 micromolar) for three days. The resulting cell-surfaceazido moieties were treated with 9 (30 micromolar) for 1 hour and thenwith avidin-AlexaFluor488 for 15 minutes at 4° C. As expected, stainingwas observed only at the surface (FIG. 8), and the labeling procedurewas equally efficient when performed at either ambient temperature or 4°C. Furthermore, blank cells exhibited very low fluorescence staining,confirming that background labeling is negligible.

Cell-surface glycoconjugates are constantly recycled by endocytosis, andto monitor this process, metabolically labeled cells were reacted with 9and avidin-AlexaFluor488 according to the standard protocol andincubated at 37° C. for 1 hour before examination by confocalmicroscopy. We observed that a significant quantity of labeledglycoproteins had been internalized into vesicular compartments.

At the completion of these studies, Bertozzi and co-workers reported adifluorinated cyclooctyne (DIFO) that reacts with azides at almost thesame reaction rate as compound 3 (Baskin et al., Proc. Natl. Acad. Sci.USA 2007, 104:16793-16797). DIFO linked to AlexaFluor was employed toinvestigate the dynamics of glycan trafficking. It was found that afterincubation for 1 hour, labeled glycans colocalized with markers forendosomes and Golgi.

4-Dibenzocyclooctynols such as 3 and 9 have several advantageousfeatures for researchers such as ease of chemical synthesis and thepossibility to further enhance the rate of cycloaddition byfunctionalization of the aromatic moieties. Modifying the aromatic ringsmay also offer an exciting opportunity to obtain reagents that becomefluorescent upon [3+2] cycloaddition with azido-containing compounds,which will make it possible to monitor in real time the trafficking ofglycoproteins and other biomolecules in living cells.

General Methods and Materials

Chemicals were purchased from Aldrich and Fluka and used without furtherpurification. Dichloromethane was distilled from CaH₂ and stored overmolecular sieves 4 Å. Pyridine was distilled from P₂O₅ and stored overmolecular sieves 4 Å. THF was distilled form sodium. All reactions wereperformed under anhydrous conditions under an atmosphere of Argon.Reactions were monitored by thin layer chromatography (TLC) on Kieselgel60 F254 (Merck). Detection was by examination under ultraviolet (UV)light (254 nm) or by charring with 5% sulfuric acid in methanol. Flashchromatography was performed on silica gel (Merck, 70-230 mesh).latrobeads (60 micrometers) were purchased from Bioscan. ¹H NMR (1D, 2D)and ¹³C NMR were recorded on a Varian Merc 300 spectrometer and onVarian 500 and 600 MHz spectrometers equipped with Sun workstations. ¹Hand ¹³C NMR spectra were recorded in CDCl₃, and chemical shifts (6) aregiven in ppm relative to solvent peaks (¹H, δ7.24; ¹³C, δ 77.0) asinternal standard for protected compounds. Negative ion matrix assistedlaser desorption ionization time of flight (MALDI-TOF) were recorded ona VOYAGER-DE Applied Biosystems using dihydrobenzoic acid as a matrix.High-resolution mass spectra were obtained using a VOYAGER-DE AppliedBiosystems in the positive mode by using 2,5-dihydroxyl-benzoic acid inTHF as matrix.

3-tert-Butyl-dimethylsilyl-oxy-1,2:5,6-dibenzocycloocta-1,5,7-triene (5)text-Butyl dimethyl silyl chloride (3.0 g, 20 mmol) was added to astirred solution of 4 (2.2 g, 10 mmol) in a mixture of CR2Cl₂ (20 mL)and pyridine (5 mL). After stirring for 6 hours at room temperature, thereaction mixture was diluted with water and extracted with CH₂Cl₂ (40mL). The combined organic extracts were washed with water and brine andthen dried (MgSO₄). The solvents were evaporated under reduced pressureand the residue was purified by silica gel column chromatography(hexane/ethyl acetate, 7/1, v/v) to afford 5 (2.9 g, 87%). ¹H NMR (300MHz, CDCl₃): δ 7.60 (1H, aromatics), 7.32-7.11 (7H, aromatics), 6.93(1H, d, J=7.5 Hz, CH═CH), 6.85 (1H, d, J=7.5 Hz, CH═CH), 5.51 (1H, dd,J=6.3, 9.6 Hz, CHOSi), 3.54 (1H, dd, J=6.3, 9.6 Hz, CH₂), 3.21 (1H, dd,J=6.3, 9.6 Hz, CH), 0.96 (3H, s, CH₃), 0.95 (3H, s, CH₃), 0.94 (3H, s,CH₃), 0.10 (3H, s, CH₃), 0.07 (3H, s, CH₃); ¹³C NMR (75 MHz, CDCl₃): δ148.0, 141.6, 140.8, 139.2, 138.3, 135.5, 135.0, 134.9, 133.0, 131.9,131.6, 130.9, 130.8, 130.2, 77.0, 52.1, 34.5, 30.7, 30.5, 23.1, 5.8,0.1; MALDI HRMS: m/z 359.1811 [M+ Na+]. Calcd for C₂₂H₂₈NaOSi 359.1807.3-Hydroxy-7,8-dibromo-1,2:5,6-dibenzocyclooctene (6)

A solution of bromine (0.8 g, 5 mmol) in CHCl₃ was added dropwise to asolution of 5 (1.7 g, 5 mmol) in CHCl₃ (30 mL) at 0° C. The reactionmixture was stirred at room temperature for 12 hours until the reactionwas complete (monitored by TLC). The resulting mixture was washed withaqueous saturated sodium thiosulfate solution (15 mL), and dried(MgSO₄). The solvents were evaporated under reduced pressure and theresidue was purified by silica gel column chromatography (hexane/CH₂Cl₂,7/1, v/v) to afford 6 (1.2 g, 60%). ¹H NMR (300 MHz, CDCl₃): δ 7.54-7.47(2H, aromatics), 7.31-6.72 (6H, aromatics), 5.77 (1H, d, J=5.4 Hz,CHBr), 5.22 (1H, dd, J=3.6, 15.9 Hz, CHOH), 5.19 (1H, d, J=5.4 Hz,CHBr), 3.50 (1H, dd, J=3.6, 15.9 Hz, CH₂), 2.75 (1H, dd, J=3.6, 15.9 Hz,CH₁); ¹³C NMR (75 MHz, CDCl₃): δ 141.3, 140.0, 137.2, 134.0, 133.4,131.5, 131.3, 130.9, 127.8, 126.2, 123.7, 121.3, 76.5, 70.0, 62.3, 32.2;MALDI HRMS: m/z 402.9313 [M+ Na+]. Calcd for C₁₆H₁₄Br₂NaO 402.9309.

3-Hydroxy-7,8-didehydro-1,2:5,6-dibenzocyclooctene (3)

To a solution of 6 (1.1 g, 3 mmol) in tetrahydrofuran (50 mL) was addeddropwise lithium diisopropylamide in tetrahydrofuran (2.0 M), (5 mL)under an atmosphere of Argon at room temperature. The reaction mixturewas stirred for 2 hours at room temperature, after which it was pouredinto ice water (50 mL) and the resulting mixture was extracted withCH₂Cl₂ (2×100 mL). The combined extracts were washed with water andbrine and then dried (MgSO₄). The solvents were evaporated under reducedpressure and the residue purified by silica gel column chromatography(hexane/ethyl acetate, 5/1, v/v) to afford 3 (0.30 g, 45%). ¹H NMR (300MHz, CDCl₃): δ 7.67 (1H, aromatics), 7.37-7.18 (7H, aromatics), 4.57(1H, dd, J=2.1, 14.7 Hz, CHOH), 3.04 (1H, dd, J=2.1, 14.7 Hz, CH₂), 2.86(1H, dd, J=2.1, 14.7 Hz, CH₂); ¹³C NMR (75 MHz, CDCl₃): δ154.5, 150.6,128.6, 127.1, 1127.0, 126.0, 125.8, 125.1, 124.7, 123.0, 122.7, 121.7,111.9, 109.6, 74.2, 47.7.

Carbonic acid 7,8-didehydro-1,2:5,6-dibenzocyclooctene-3-yl ester4-nitrophenyl ester (7)

To a solution of 3 (0.22 g, 1 mmol) in CH₂Cl₂ (30 mL) was added4-nitro-phenyl chlorofonnate (0.4 g, 2 mmol) and pyridine (0.4 ml, 5mmol). After stirring 4 hours at ambient temperature, the reactingmixture was washed with brine (2×10 mL), and the organic layer was dried(MgSO₄). The solvents were evaporated under reduced pressure, and theresidue was purified by silica gel column chromatography (hexane/ethylacetate, 10/1, v/v) to afford 7 (0.34 g, 89%). ¹H NMR (300 MHz, CDCl₃):δ 8.23-8.18 (2H, aromatics), 7.56-7.54 (2H, aromatics), 7.46-7.18 (8H,aromatics), 5.52 (1H, dd, J=3.9, 15.3 Hz, CHOH), 3.26 (1H, dd, J=3.9,15.3 Hz, CH₂), 2.97 (1H, dd, J=3.9, 15.3 Hz, CH₂); ¹³C NMR (75 MHz,CDCl₃): δ 154.5, 150.7, 149.1, 148.7, 129.0, 127.4, 127.3, 126.7, 126.5,125.5, 125.2, 124.3, 124.0, 122.6, 122.4, 120.8, 120.6, 120.2, 112.2,108.5, 80.6, 44.8; MALDI HRMS: m/z 408.0852 [M+ Na+]. Calcd forC₂₃H₁₅NNaO₅ 408.0848.

Carbonic acid 7,8-didehydro-1,2:5,6-dibenzocyclooctene-3-yl ester,8′-biotinylamine-3′,6′-dioxaoctane l′-amide (9)

To a solution of 8 (37 mg, 0.1 mmol) and NEt₃ (30 mg, 0.3 mmol) in DMF(10 mL) was added 7 (39 mg, 0.1 mmol) under an atmosphere of Argon.After stirring the reaction mixture overnight at ambient temperature,the solvent was removed under reduced pressure and the residue waspurified by silica gel column chromatography (CH₂Cl₂/CH₃OH, 20/1, v/v)to afford 9 (44 mg, 71%). ¹H NMR (500 MHz, CD₃OD): δ 7.59 (1H,aromatics), 7.42-7.33 (7H, aromatics), 5.44, (1H, dd, J=5.0, 14.1 Hz,CHOH), 4.60, 4.46 (m, 2H, CHNH), 4.24 (s, 4H, OCH₂CH₂O), 3.72 (m, 4H,OCH₂), 3.64 (m, 2H, CH₂NH), 3.55 (m, 1H, CHS), 3.33 (dd, 1H, J1=12.0 Hz,J2=4.8 Hz, 1H, CHHexoS), 3.23 (t, 2H, J=6 Hz, CH₂—NH₂), 3.22, (1H, dd,J=5.0, 14.1 Hz, CH₂), 2.88, (1H, dd, J=5.0, 14.1 Hz, CH₂), 2.68 (d, 1H,J=12.45 Hz, CHHendoS), 2.20 (t, 2H, J=7.5 Hz, CH₂CO), δ 1.4 (m, 6H,biotin-CH₂). ¹³C NMR (75 MHz, CD₃OD): δ 175.0, 164.9, 156.9, 152.5,151.3, 129.9, 128.2, 128.1, 127.2, 127.1, 126.0, 125.7, 123.8, 121.2,112.7, 109.8, 76.8, 70.2, 70.1, 69.8, 69.4, 62.1, 60.4, 55.8, 54.6,46.0, 42.6, 40.6, 39.9, 39.1, 35.5, 28.6, 28.3, 25.6, 17.5, 16.1, 12.0;MALDI HRMS: m/z 643.2575 [M+ Na+]. Calcd for C₃₃H₄₀N₄NaO₆S 643.2566.

General Procedure for Click Reactions with Carbohydrates and Peptides

3-Hydroxy-7,8-didehydro-1,2:5,6-dibenzocyclooctene (2.2 mg, 0.01 mmol)was dissolved in CH₃OH (1 mL) and an azide (3-azidopropyl2,3,4,6-tetra-O-acetate-α-D-mannopyranoside,1-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-4,6-O-isopropylidene-2-azido-2-deoxy-β-Dglucopyranose,4,7,8-tri-O-acetyl-5-acetamido-9-azido-2,3-anhydro-3,5,9-tri-deoxy-D-glycero-D-galacto-non-2-enonicmethyl ester, and4-azido-N-[(1,1-dimethylethoxy)carbonyl]-Lphenylalanine, 1.0equivalents) was added. The reaction was monitored by TLC, and afterstirring the reaction mixture for 30 minutes at room temperature, thereaction had gone to completion. The solvents were evaporated underreduced pressure and the residue was purified by silica gel columnchromatography to afford the desired products 10-13 respectively inquantitative yields.

Compound 10; ¹H NMR (500 MHz, CDCl₃): δ 7.83 (1H, m, aromatics),7.58-6.99 (7H, m, aromatics), 5.33-4.98 (4H, m, 2-H, 3-H, 4-H, CHOH),4.90-4.61 (1H, m, 1-H), 4.26, 4.10 (2H, m, 6-H), 3.93 (1H, m, 5-H),3.70-3.60 (2H, m, OCH₂CH₂), 3.58-3.41 (2H, m, CH2N), 3.31, 3.20, 3.06,2.91 (2H, m, CHOHCH₂), 2.35-1.94 (12H, m, CH₃CO), 1.38-1.14 (2H, m,CH₂CH₂N); ¹³C NMR (75 MHz, CDCl₃): δ 170.9, 170.2, 148.5, 146.9, 145.5,144.9, 141.2, 139.3, 138.0, 136.7, 135.5, 133.8, 133.0, 132.3, 131.6,130.3, 129.5, 129.0, 128.3, 127.7, 127.2, 126.5, 125.0, 124.2, 98.0,97.4, 70.1, 69.5, 68.8, 66.2, 65.4, 64.9, 64.4, 62.6, 47.0, 45.1, 40.5,32.1, 31.1, 30.6, 29.9, 22.9, 20.9, 14.3; MALDI HRMS: m/z 674.2330 [M+Na+]. Calcd for C₃₃H₃₇N₃NaO₁₁ 674.2326.

Compound 11; ¹HNMR (500 MHz, CDCl₃): δ 7.80, 7.65 (1H, d, J=7.5Hz,aromatics), 7.48-7.06 (7H, aromatics), 5.82, 5.72, 5.60, 5.48 (1H, d,J=7.09 Hz, 1-H), 5.13-4.60 (1H, m, CHOH), 4.40-4.20 (2H, m, 2-H, 3-H),4.10-3.90 (2H, m, 5-H, 6-H), 3.89-3.63 (1H, m, 6-H), 3.54-3.40 (2H, m,4-H, HCHCHOH), 3.07, 2.66 (1H, m, HCHCHOH), 1.54-1.20 (6H, m,CH(CH₃)C(CH₃)₂), 0.98-0.60 (13H, m, 2CH₃, CH(CH₃)₂), 0.35-0.19 (6H, m,Si(CH₃)₂); ¹³C NMR (75 MHz, CDCl₃): δ 151.0, 149.2, 148.5, 148.0, 146.1,145.3, 142.4, 141.6, 140.8, 139.4, 138.1, 136.6, 135.7, 134.9, 133.4,132.4, 131.6, 130.6, 129.5, 128.9, 127.3, 103.5, 100.4, 99.8, 80.6,73.3, 70.9, 69.3, 68.8, 65.5, 50.1, 46.6, 45.4, 44.4, 37.3, 33.3, 32.5,28.4, 23.4, 22.6, 21.9, 4.6, 1.4, 0.7, 0.0; MALDI HRMS: m/z 630.2980 [M+Na+]. Calcd for C₃₃H₄₅N₃NaO₆Si 630.2975.

Compound 12; ¹H NMR (500 MHz, CDCl₃): δ 7.95-7.69 (1H, m, aromatics),7.60-7.03 (7H, m, aromatics), 6.77-6.26 (1H, m), 5.98-8.81 (1H, m),5.80-5.61 (1H, m), 5.58-5.33 (1H, m), 5.32-5.16 (2H, m), 5.16-4.94 (1H,rn), 4.93-4.80 (1H, m), 4.69-4.34 (1H, m), 4.24-4.06 (1H, m), 3.95-3.60(3H, m), 3.53-2.90 (2H, m), 2.32-1.57 (12H, m); ¹³C NMR (75 MHz, CDCl₃):δ 169.6, 160.5, 147.8, 145.5, 145.1, 144.6, 143.9, 140.5, 138.7, 138.2,137.1, 135.7, 134.5, 133.5, 132.7, 132.2, 131.8, 131.2, 130.8, 129.5,129.0, 128.3, 127.7, 127.2, 126.5, 125.9, 124.8, 122.7, 108.0, 107.5,75.1, 69.6, 68.8, 67.1, 66.6, 52.8, 51.7, 47.3, 46.4, 45.3, 28.7, 28.3,22.0, 19.8; MALDI HRMS: m/z 699.2282 [M+Na⁺]. Calcd for C₃₄H₃₆N₄NaO₁₁699.2278. Compound 13; ¹H NMR (300 MHz, CD30D): δ 7.8-6.8 (12H, m,aromatics), 5.33, 5.17 (1H, dd, J=5.1, 10.5 Hz CHOH), 4.37 (1H, m,CHCOOH), 3.8, 3.23 3.77, 3.20 (2H, m, CH₂CHOH), 3.21, 2.93 (2H, m,CH₂CHNH), 1.35 (9H, m, C(CH₃)₃); ¹³C NMR (75 MHz, CD3OD): δ 156.6,145.1, 414.3, 139.6, 139.4, 138.0, 137.3, 136.1, 135.3, 135.0, 133.7,133.4, 132.1, 131.7, 130.6, 130.3, 130.0, 129.5, 129.2, 128.8, 128.3,128.0, 127.6, 126.9, 126.6, 126.6, 126.2, 125.3, 125.1, 124.8, 79.4,76.8, 76.2, 68.6, 58.5, 54.9, 46.2, 40.5, 37.1, 29.6, 29.3, 27.5; MALDIHRMS: m/z 549.2118 [M+ Na+]. Calcd for C₃₀H₃₀N₄NAO 549.2114.

N-Boc-3,6-dioxaoctczne-1,8-diamine

A solution of di-tert-butyl dicarbonate (di-Boc) (6 g, 28 mmol, 0.5equiv) in CH₂Cl₂ (100 mL) was added dropwise to a mixture oftris(ethylene glycol)-1,8-diamine (7.6 g, 56 mmol) anddiisopropylethylamine (10 mL, 57 mmol) at room temperature over a periodof 2 hours. The reaction mixture was stirred for 6 hours, after which itwas concentrated in vacuo. Purification by flash silica gel columnchromatography (CH₂Cl₂/CH₃OH, 10/1, v/v) affordedN-Boc-3,6-dioxaoctane-1,8-diamine (4.1 g, 58%). ¹H NMR (300 MHz, CD3OD):δ 3.6 (s, 4H), 3.54 (t, 2H), 3.53 (t, 2H), 3.24 (t, 2H), 2.8 (t, 2H),1.4 (s, 9H); MALDI HRMS: m/z 271.1641 [M+ Na+]. Calcd for C₁₁H₂₄N₂NaO₄271.1634.

N-Boc-N′-biotinyl-3,6-dioxaoctane-1,8-diamine

A solution of vitamin H (Biotin) (2.2 g, 9 mmol),O-benzotriazol-1-yl-N,N,N′, N′-tetramethyluronium hexafluorophosphate(HBTU) (3 g, 8 mmol), and DIPEA (1.8 mL, 10 mmol) in DMF (100 mL) wasstirred for 10 minutes at room temperature before being adding dropwiseto a solution of N-Boc-3,6-dioxaoctane-1,8-diamine (1.5 g, 6 mmol, 1).The reaction mixture was stirred for 1 hour at room temperature, afterwhich the DMF was removed in vacuo to give an oily residue, which waspurified by flash silica gel column chromatography (CH₂Cl₂/CH₃OH, 25/1,v/v) to afford N-Boc-N′-biotinyl-3,6-dioxaoctane-1,8-diamine (2.0 g,90%). ¹H NMR (300 MHz, CD₃OD): δ 4.5 (m, 1H), 4.3 (m, 1H), 3.6 (s, 4H),3.54 (tt, 4H), 3.39 (t, 2H), 3.26 (t, 2H), 2.9 (dd, 1H), 2.7 (d, 1H),2.2 (t, 2H), 1.7-1.5 (m, 8H), 1.4 (s, 9H); MALDI HRMS: m/z 497.2416 [M+Na+]. Calcd for C₂₁H₃₈N₄NaO₆S 497.2410.

N-Biotinyl-3,6-dioxaoctane-1,8-diamine (8)N-Boc-N′-biotinyl-3,6-dioxaoctane-1,8-diamine (1.9 g, 4 mmol) wasdissolved in 50% TFA in CH₇C1, (20 mL) and stirred for 1 hour at roomtemperature. The solvents were evaporated under reduced pressure to givean oily residue, which was purified by flash silica gel columnchromatography (CH7C12/CH₃OH, 10/1, v/v) to afford 7 (1.3 g, 92%). ¹HNMR (300 MHz, DMSO-d6): δ 7.85 (t, 1H, J=5.7 Hz, NHCO), 6.42, 6.35 (s,2H, NH), 4.29, 4.11 (m, 2H, CHNH), 3.5 (s, 4H, OCH2CH₂O), 3.3 (m, 4H,OCH₂), 3.16 (m, 2H, CH₂NH), 3.10 (m, 1H, CHS), 2.81 (dd, 1H, J1=12.0 Hz,J2=4.8 Hz, 1H, CHHexoS), 2.64 (t, 2H, J=6 Hz, CH₂—NH₂), 2.52 (d, 1H,J=12.45 Hz, CHHendoS), 2.06 (t, 2H, J=7.5 Hz, CH₂CO), 1.6 (s, 2H, NH₂),δ 1.4 (m, 6H, biotin-CH₂); ¹³C NMR (75 MHz, DMSO-d₆): δ 171.9, 160.6,71.7, 71.6, 69.5, 69.1, 64.4, 59.2, 55.0, 54.2, 40.7, 38.4, 35.1, 28.4,28.1, 25.2; MALDI HRMS: m/z 397.1892 [M+ Na+]. Calcd for C₁₆H₃₀N₄NaO₄S397.1885. Reagents for Biological Experiments

Synthetic compounds 2 and 9 were reconstituted in DMF and stored at 80°C. Final concentrations of DMF never exceeded 0.56% to avoid toxiceffects.

Cell surface azide labeling and detection by fluorescence intensity

Human Jurkat cells (Clone E6-1; ATCC) were cultured in RPMI 1640 medium(ATCC) with L-glutamine (2 mM), adjusted to contain sodium bicarbonate(1.5 g L⁻¹), glucose (4.5 g L⁻¹), HEPES (10 mM), and sodium pyruvate(1.0 mM) and supplemented with penicillin (100 u mL⁻¹)/streptomycin (100micrograms mL⁻¹; Mediatech) and fetal bovine serum (FBS, 10%; Hyclone).Cells were maintained in a humid 5% CO, atmosphere at 37° C. Jurkatcells were grown in the presence of peracetylatedN-azidoacetylmannosamine (Ac4ManNaz; 25 micromolar final concentration)for 3 days, leading to the metabolic incorporation of the correspondingN-azidoacetyl sialic acid (SiaNAz) into their cell surfaceglycoproteins. Jurkat cells bearing azides and untreated control cellswere incubated with the biotinylated compounds 2 and 9 (0-100micromolar) in labeling buffer (DPBS, supplemented with FBS (1%)) for0-180 minutes at room temperature. The cells were washed three timeswith labeling buffer and then incubated with avidin conjugated withfluorescein (Molecular Probes) for 15 minutes at 4° C. Following threewashes and cell lysis, cell lysates were analysed for fluorescenceintensity (485 ex/520 em) using a microplate reader (BMG Labtech). Datapoints were collected in triplicate and are representative of threeseparate experiments. Cell viability was assessed at different points inthe procedure with exclusion of trypan blue.

Cell labeling and detection by fluorescence microscopy

Chinese hamster ovary (CHO) cells (Clone KI; ATCC) were cultured inKaighn's modification of Ham's F-12 medium (F-12K) with L-glutamine (2mM), adjusted to contain sodium bicarbonate (1.5 g L⁻¹) and supplementedwith penicillin (100 u mL⁻¹)/streptomycin (100 micrograms mL⁻¹ and FBS(10%). Cells were maintained in a humid 5% CO₂ atmosphere at 37° C. CHOcells were grown in the presence of Ac4ManNaz (100 micromolar finalconcentration) for 3 days to metabolically incorporate SiaNAz into theircell surface glycoproteins. CHO cells bearing azides and untreatedcontrol cells were then transferred to a glass coverslip and culturedfor 36 hours in their original medium. Live CHO cells were treated withthe biotinylated compound 9 (30 micromolar) in labeling buffer (DPBS,supplemented with FBS (1%)) for 1 hour at 4° C. or at room temperature,followed by incubation with avidin conjugated with Alexa Fluor 488(Molecular Probes) for 15 minutes at 4° C. Cells were washed 3 timeswith labeling buffer and fixed with formaldehyde (3.7% in PBS) orincubated for 1 hour at 37° C. before fixation. The nucleus was labeledwith the far red fluorescent TO-PRO-3 dye (Molecular Probes). The cellswere mounted with PennaFluor (Thermo Electron Corporation) beforeimaging. Initial analysis was performed on a Zeiss Axioplan2 fluorescentmicroscope. Confocal images were acquired using a 60×(NA1.42) oilobjective. Stacks of optical sections were collected in the zdimensions. The step size, based on the calculated optimum for eachobjective, was between 0.25 and 0.5 micrometers. Subsequently, eachstack was collapsed into a single image (z-projection). Analysis wasperformed offline using ImageJ 1.39f software (National Institutes ofHealth, USA) and Adobe Photoshop CS3 Extended Version 10.0 (AdobeSystems Incorporated), whereby all images were treated equally.

Example 2 Alkyne Reagents Containing Biotin and a Cleavable Linker

Azides, which are extremely rare in biological systems, are emerging asattractive chemical handles for bioconjugation (Dedola et al., Org.Biomol. Chem. 2007, 5, 1006; Kolb and Sharpless, Drug Dis. Today 2003,8, 1128; Moses and Moorhouse, Chem. Soc. Rev. 2007, 36, 1249; Nandivadaet al., Adv. Mater. 2007, 19, 2197; Wu and Fokin, Aldrichimica ACTA2007, 40, 7; Agard et al., ACS Chem. Biol. 2006, 1, 644). In particular,the Cu(I) catalyzed 1,3-dipolar cyclization of azides with terminalalkynes to give stable triazoles has been employed for tagging a varietyof biomolecules including proteins, nucleic acids, lipids, andsaccharides (Chin et al., Science 2003, 301, 964; Gierlich et al., Org.Lett. 2006, 8, 3639; Kho et al., Proc. Natl. Acad. Sci. 2004, 101,12479; Link et al., Proc. Natl. Acad. Sci. 2006, 103, 10180; Wang etal., J. Am. Chem. Soc. 2003, 125, 3192). The cycloaddition has also beenused for activity-based protein profiling (Speers et al., J. Am. Chem.Soc. 2003, 125, 4686), monitoring of enzyme activity, and the chemicalsynthesis of microarrays and small molecule libraries (Sun et al.,Bioconjugate Chem. 2006, 17, 52).

An attractive approach for installing azides into biomolecules is basedon metabolic labeling whereby an azide containing biosynthetic precursoris incorporated into biomolecules using the cells' biosyntheticmachinery (Prescher and Bertozzi, Nat. Chem. Biol. 2005, 1,13). Thisapproach has been employed for tagging proteins, glycans, and lipids ofliving systems with a variety of reactive probes. These probes canfacilitate the mapping of saccharide-selective glycoproteins andidentify glycosylation sites (Hanson et al., J. Am. Chem. Soc. 2007,129, 7266). Alkyne probes have also been used for cell surface imagingof azide-modified bio-molecules and a particularly attractive approachinvolves the generation of a fluorescent probe from a non-fluorescentprecursor by a [3+2] cycloaddition (Sivakumar et al., Org. Lett. 2004,6, 4603).

We describe here reagents including an alkyne fragment, a cleavablelinker fragment, and biotin. Such compounds are expected to be valuablefor biological research. Thus, the alkyne fragment of the reagent canreact with various biomolecules containing an azide fragment to givestable triazole adducts. The biotin fragment gives an opportunity toretrieve the tagged compounds by affinity chromatography usingimmobilized avidin. The cleavable linker allows the release of taggedand captured biomolecules for analysis. For example, released proteinsor glycoproteins can be characterized by standard proteomics orglycomics analysis (Too, Expert Rev. Proteomics 2007, 4, 603; Bantscheffet al., Anal. Bioanal. Chem. 2007, 389, 1017; Lau et al., Proteomics2007, 7, 2787). Release of the proteins and glycoproteins is much morepractical than previously reported analysis of biomolecules attached toimmobilized avidin (Hanson et al., J. Am. Chem. Soc. 2007, 129, 7266).Compound 21 is an example of the new class of reagent (FIG. 9). Itcontains a 4-dibenzocyclooctynol fragment for reaction with azides, adisulfide, which can be cleaved with reducing reagents such asdithiothreitol (DTT), and biotin.

The quantification of differences between physiological states of abiological system is a technically challenging task in proteomics (Too,Expert Rev. Proteomics 2007, 4, 603; Bantscheff et al., Anal. Bioanal.Chem. 2007, 389, 1017; Lau et al., Proteomics 2007, 7, 2787). Inaddition, to the classical methods of differential protein gel or blotstaining by dyes and fluorophores, mass-spectrometry-basedquantification methods is gaining popularity. Most of the latter methodsemploy differential stable isotope labeling to create a specific masstag that can be recognized by a mass spectrometer and at the same timeprovide the basis for quantification. These mass tags can be introducedinto proteins or peptides by (i) metabolical labeling, (ii) by chemicalmeans, (iii) enzymatically, or (iv) by spiking with synthetic peptidestandards.

Reagents composed of an alkyne, a cleavable linker and biotin can beemployed to introduce mass tags into proteins, glycoproteins and otherbiomolecules containing an azide fragment. Thus, by employing reagentssuch as 21 and 22, different mass tags can be introduced to quantifyproteins, glycoproteins, glycopeptides, peptides and carbohydrates. Thechemical synthesis of 21 and 22 is depicted in Schemes 4 and 5,respectively (FIGS. 10 and 11). Various alkyne moieties, cleavablelinkers and biotin derivatives are depicted in FIG. 12 and alkyne andreactive diene derivatives are depicted in FIG. 13.

Example 3 Fast Click Reactions for Labeling of Living Cells andNanoparticles

An alternative approach for preparing 4-dibenzcyclooctynol and usingthis compound for the preparation of amine containing click reagents.

4-Dibenzocyclooctynol 45 could be prepared by an alternative syntheticroute (Scheme 6; FIG. 14). Thus, known of dibenzosuberenone (41) wastreated trimethylsilyl diazomethane in the presence of BF₃.OEt₂ inCH₂Cl₂ (20 ml) at −10° C. to give 6H-Dibenzo[a,e]cyclooctatrien-5-one(42) in good yield. The ketone of 42 was reduced with sodium borohydridein a mixture of ethanol and THF to give alcohol 43, which could beconverted into 4-dibenzocyclooctynol 45 by bromination of the doublebond followed by elimination of the resulting compound 44 by treatmentLDA in THF. Compound 45 could be oxidized to the corresponding ketone 46by employing Dess-Martin reagent.

Compounds 45 and 46 were converted into amine containing derivatives 49,50 and 51. The attraction of these compounds is that the can easily bederivatized with various probes such as fluorescent tags and biotin.Furthermore, the amine gives an easy chemical handle for attachment topolymeric supports. Thus, alcohol 45 was converted into p-nitrophenylester 49 by reaction with 4-nitro-phenyl chloroformate (0.4 g, 2 mmol)and pyridine. The target compound compound 49 was obtained by reactionof 49 with an excess of tris(ethylene glycol)-1,8-diamine. Compound 50was obtained by reaction of 46 with bromoacetic acid in the presence oflithium diisopropylamide in tetrahydrofuran followed by condensation ofthe resulting acid 48 with tris(ethylene glycol)-1,8-diaminein DMF inthe presence of the coupling reagent HATU and the base DIPEA. Finally,derivative 51 was prepared by oxime formation be reaction of ketone 51with N-{2-[2-(2-amino-ethoxy)-ethoxy]-ethyl}-2-aminooxy-acetamide (84mg, 0.251 mmol) in the presence of acetic acid and in a mixture ofmethanol and dichloromethane. A feature of 51 is that the oxime linkagecan be cleaved by treatment with aqueous acid to detach the capturedcompound from the click reagent.

Experimental

6H-Dibenzo[a,e ]cyclooctatrien-5-one (42). To a stirred solution ofdibenzosuberenone 41 (2.888 g, 14.0 mmol) and BF₃.OEt₂ (2.59 ml, 21.0mmol) in CR₂Cl₂ (30 ml) was added dropwise a solution of trimethylsilyldiazomethane (10.5 ml, 21.9 mmol) in CH₂Cl₂ (20 ml) at −10° C. over 1hour. The mixture was stirred at −10° C. for 2 hours, and then pouredinto ice water. The aqueous layer was extracted with CH₂Cl₂ (3×100 ml)and the organic layers were combined. The combined organic layers werewashed with brine and dried (MgSO₄). The solvent was removed underreduced pressure, and the crude product was purified by flashchromatography on silica gel (2:1-1:2 v/v hexanes/CH₂Cl₂) to give theproduct as pale solid (2.220 g, 72%). ¹H NMR (300 MHz, CDCl₃): δ 8.26(1H, q, J=1.4, 6.6 Hz), 7.13-7.43 (7H, m), 7.05 (2H, q, J=3.8, 12.9 Hz),4.06 (2H, s). ¹³C NMR (75 MHz, CDCl₃): δ 196.6, 136.9, 136.3, 135.4,133.8, 133.1, 132.4, 131.4, 130.6, 129.3, 128.8, 128.0, 127.3, 126.9,48.4. MALDI HRMS: m/z [M+Na⁺]. Calcd for C₁₆H₁₂NaO: 243.0786 (Chaffins,S.; Brettreich, M.; Wudl, F. Synthesis 2002, 1191-1194).

5,6-Dihydro-dibenzo[a,e]cycloocten-5-ol (43). To a stirred solution of42 (2.203 g, 10 mmol) in 1:1 EtOH/THF (120 ml) at room temperature wasadded slowly sodium borohydride (0.757 g, 20 mmol), and the reactionmixture was stirred at room temperature for 7 hours. TLC indicated thatthe reaction was complete, and the reaction mixture was quenched by slowaddition of acetic acid (1 ml). The solvent was evaporated, and theresidue was dissolved in CH₂Cl₂ (100 ml) and brine (100 ml), extractedwith CH₂Cl₂ (4×100 ml). The organic phase was combined, dried (MgSO₄)and evaporated to give the product as white solid (2.223 g, 100%), whichis directly used in the next step reaction without further purification.¹H NMR (300 MHz, CDCl₃): δ 7.50 (1H, m), 7.14-7.30 (7H, m), 6.90 (2H, q,J=2.7, 12.0 Hz), 5.31 (1H, q, J=6.3, 10.0 Hz), 3.41 (2H, m). ¹³C NMR (75MHz, CDCl₃): δ 141.7, 136.7, 136.2, 134.5, 131.7, 131.5, 130.1, 129.9,129.3, 128.7, 127.4, 127.2, 126.9, 125.9, 74.4, 42.7. MALDI HRMS: m/z[M+Na⁺]. Calcd for C₁₆H₁₄NaO: 245.0942.

11,12-Dibromo-5,6, 11,12-tetrahydro-dibenzo [a,e]cycloocten-5-ol (44).To a stirred solution of 43 (2.223 g, 10 mmol) in 1:1 CHCl₃ (50 ml) atroom temperature was added dropwise bromine (0.512 ml, 10 mmol), and thereaction mixture was stirred at room temperature for 0.5 hour TLCindicated that the reaction was complete, and the solvent was removed atroom temperature under reduced pressure. The residue was purified byflash chromatography on silica gel (2:1-1:2 v/v hexanes/CH₂Cl₂) to givethe product as yellowish oil (2.220 g, 58%). ¹HNMR (300 MHz, CDCl₃): δ7.54-7.47 (2H, aromatics), 7.31-6.72 (6H, aromatics), 5.77 (1H, d, J=5.4Hz, CHBr), 5.22 (1H, dd, J=3.6, 15.9 Hz, CHOH), 5.19 (1H, d, J=5.4 Hz,CHBr), 3.50 (1H, dd, J=3.6, 15.9 Hz, CH₂), 2.75 (1H, dd, J=3.6, 15.9 Hz,CH₂). ¹³C NMR (75 MHz, CDCl₃): δ 141.3, 140.0, 137.2, 134.0, 133.4,131.5, 131.3, 130.9, 127.8, 126.2, 123.7, 121.3, 76.5, 70.0, 62.3, 32.2.MALDI HRMS: m/z 402.9313 [M+Na⁺]. Calcd for C₁₆H₁₄Br₂NaO: 402.9309.

5,6-Dihydro-11,12-didehydro-dibenzo[a,e1]cycloocten-5-ol (45). To astirred solution of 44 (1.528 g, 4 mmol) in tetrahydrofuran (40 ml) wasadded dropwise lithium diisopropylamide in tetrahydrofuran (2.0 M) (8ml, 16 mmol) under an atmosphere of Argon at room temperature. Thereaction mixture was stirred for 0.5 hour at room temperature, afterwhich it was quenched by addition of dropwise water (0.5 ml). Thesolvents were evaporated under reduced pressure, and the residue waspurified by flash chromatography on silica gel (2:1-0:1 v/vhexanes/CH₂Cl₂) to give the product as white solid (0.503 g, 57%). ¹HNMR (300 MHz, CDCl₃): δ 7.67 (1H, aromatics), 7.37-7.18 (7H, aromatics),4.57 (1H, dd, J=2.1, 14.7 Hz, CHOH), 3.04 (1H, dd, J=2.1, 14.7 Hz, CH₂),2.86 (1H, dd, J=2.1, 14.7 Hz, CH₂). ¹³C NMR (75 MHz, CDCl₃): δ154.5,150.6, 128.6, 127.1, 1127.0, 126.0, 125.8, 125.1, 124.7, 123.0, 122.7,121.7, 111.9, 109.6, 74.2, 47.7.

6H-11,12-Didehydro-dibenzo [a,e]cyclooctatrien-5-one (46). To a stirredsolution of 45 (0.172 g, 0.781 mmol) in CH₂Cl₂ (40 ml) was addedDess-Martin reagent (0.397 g, 0.937 mmol). The reaction mixture wasstirred for 0.5 hour at room temperature, TLC indicated that thereaction was complete. The reaction mixture was filter through a shortpad of silica gel, and washed with CH₂Cl₂. The filtrate wasconcentrated, and the residue was purified by flash chromatography onsilica gel (1:1-0:1 v/v hexanes/CH₂Cl₂) to give the product as whitesolid (0.158 g, 93%). ¹H NMR (300 MHz, CDCl₃): δ 7.29-7.57 (8H, m), 4.17(1H, d, J=10.6 Hz), 3.64 (1H, J=10.6 Hz). ¹³C NMR (75 MHz, CDCl₃): δ200.4, 154.7, 148.2, 131.21 (2 C), 131.18, 129.3, 128.2, 127.8, 126.3,125.9, 122.2, 111.1, 109.4, 49.3.

MALDI HRMS: m/z [M+Na⁺]. Calcd for C₁₆H₁₀NaO: 241.0629.

Carbonic acid 5,6-dihydro-11,12-didehydro-dibenzo[a,e]cycloocten-5-ylester 4-nitro-phenyl ester (47). To a solution of 45 (0.22 g, 1 mmol) inCH₂Cl₂ (30 mL) was added 4-nitro-phenyl chloroformate (0.4 g, 2 mmol)and pyridine (0.4 ml, 5 mmol). After stirring 4 hours at ambienttemperature, the reacting mixture was washed with brine (2×10 mL), andthe organic layer was dried (MgSO₄). The solvents were evaporated underreduced pressure, and the residue was purified by silica gel columnchromatography (hexane/ethyl acetate, 10/1, v/v) to afford 47 (0.34 g,89%). ¹H NMR (300 MHz, CDCl₃): δ 8.23-8.18 (2H, aromatics), 7.56-7.54(2H, aromatics), 7.46-7.18 (8H, aromatics), 5.52 (1H, dd, J=3.9, 15.3Hz, CHOH), 3.26 (1H, dd, J=3.9, 15.3 Hz, CH₂), 2.97 (1H, dd, J=3.9,15.3Hz, CH₂). ¹³C NMR (75 MHz, CDCl₃): δ 154.5, 150.7, 149.1, 148.7,129.0, 127.4, 127.3, 126.7, 126.5, 125.5, 125.2, 124.3, 124.0, 122.6,122.4, 120.8, 120.6, 120.2, 112.2, 108.5, 80.6, 44.8. MALDI HRMS: m/z408.0852 [M+ Na⁺]. Calcd for C₂₃H₁₅NNaO₅: 408.0848.

(5,6-Dihydro-11,12-didehydro-dibenzo[a,e]cycloocten-5-yloxy)-acetic acid(48). To a stirred solution of bromoacetic acid (0.280 g, 2 mmol) intetrahydrofuran (40 ml) at 0° C. was added slowly sodium hydride (60%oil dispersion, 0.120 g, 3.0 mmol). The mixture was stirred at 0° C. for10 minutes, then 45 (0.220 g, 1.0 mmol) was added. The mixture wasstirred at 0° C. for another 10 minutes, then warmed to room temperatureand stirred for 1 day. The reaction was quenched by 1 drop of HOAc,filtered through a short pad of silica gel washed by EtOAc, thenconcentrated under reduced pressure. The residue was purified by flashchromatography on silica gel (1:0-1:1 CH₂Cl₂/EtOAc) to give the productas white solid (0.60 g, 22%). ¹H NMR (300 MHz, CDCl₃): δ 7.69 (1H, d,J=7.7 Hz), 7.49 (1H, d, J=6.7 Hz), 7.41 (1H, m), 7.27-7.35 (5H, m), 4.25(1H, m), 4.15 (2H, d, J=8.0 Hz), 3.30 (1H, dd, J=2.2, 14.8 Hz), 2.72(1H, dd, J=3.6, 14.8 Hz). ¹³C NMR (75 MHz, CDCl₃): δ 154.5, 150.6,128.6, 127.1, 1127.0, 126.0, 125.8, 125.1, 124.7, 123.0, 122.7, 121.7,111.9, 109.6, 74.2, 47.7.MALDI HRMS: m/z 301.0838 [M+Na⁺]. Calcd forC₁₈H₁₄NaO₃: 301.0841.

{2-[2-(2-Amino-ethoxy)-ethoxy]ethyl}-carbamic acid5,6-dihydro-11,12-didehydro-dibenzo[a,e]cycloocten-5-yl ester (49). To astirred solution of 47 (0.077 g, 0.2 mmol) and tris(ethyleneglycol)-1,8-diamine (0.293 ml, 2 mmol) in CH₂Cl₂ (20 ml) at roomtemperature was added Et₃N (0.139 ml, 1.0 mmol). The reaction mixturewas stirred for 3 hours at room temperature, after which the solvent wasremoved under reduced pressure. The residue was purified by flashchromatography on Iatrobeads (8-30% v/v MeOH/CH₂Cl₂) to give the productas yellowish solid (0.063 g, 80%). ¹H NMR (300 MHz, CDCl₃): δ 7.51 (1H,d, J=7.3 Hz), 7.24-7.37 (7H, m), 5.81 (1H, s, NH), 5.48, (1H, br),3.50-3.68 (8H, m), 3.39 (2H, m), 3.16 (1H, d, J=14.8 Hz), 2.91 (2H, br),2.88 (1H, d, J=14.8 Hz), 2.57 (2H, br, NH₂). ¹³C NMR (75 MHz, CDCl₃): δ155.7, 152.2, 151.1, 130.0, 128.1, 128.0, 127.2, 127.1, 126.3, 126.0,123.9, 123.8, 121.3, 113.0, 110.0, 76.7, 72.8, 70.3, 70.2, 70.1, 70.0,46.2, 41.5, 41.0. MALDI HRMS: m/z 417.1746 [M+Na⁺]. Calcd forC₂₃H₂₆N₂NaO₄: 417.1790.

N-{2-[2-(2-Amino-ethoxy)-ethoxy]-ethyl}-2-(5,6-dihydro-11,12-didehydro-dibenzo[a,e]cycloocten-5-yloxy)-acetamide(50). To a stirred solution of 48 (5.6 mg, 0.02 mmol) and tris(ethyleneglycol)-1,8-diamine (0.0292 ml, 0.2 mmol) in DMF (3 ml) at roomtemperature was added HATU coupling reagent (7.6 mg, 0.02 mmol) andDIPEA (0.0348 ml, 0.2 mmol). The reaction mixture was stirred for 2hours at room temperature, after which the solvent was removed underreduced pressure. The residue was purified by flash chromatography onIatrobeads (8-30% v/v MeOH/CH₂Cl₂) to give the product as colorless oil.MALDI HRMS: m/z 431.1916 [M+Na⁺]. Calcd for C₂₄H₂₈N₂NaO₄: 431.1947.

N-{2-[2-(2-Amino-ethoxy]-ethyl}-2-(6H-11,12-didehydro-dibenzo[a,e]cycloocten-5-ylideneaminooxy)-acetamide(51). A solution of 46 (46 mg, 0.211 mmol),N-{2-[2-(2-amino-ethoxy)-ethoxy]-ethyl}-2-aminooxy-acetamide (84 mg,0.251 mmol) and acetic acid (0.1 ml) in 1:1 v/v MeOH/CH₂Cl₂ (4 ml) wasstirred at room temperature for 2 days. The solvent was removed underreduced pressure, and the residue was purified by flash chromatographyon Iatrobeads (4-15% v/v MeOH/CH₂Cl₂) to give the product as yellowishsolid.(56 mg, 63%). MALDI HRMS: m/z 444.1835 [M+Na⁺]. Calcd forC₂₄H₂₇N₃NaO₄: 444.1899.

Reaction kinetics of cycloaddition of derivatives of4-dibenzocyclooctynol.

A number of analogs (63-68) of 4-dibenzocyclooctynol (61) were preparedand the influence of these modifications on the reaction rate of thecycloaddition with benzyl azide was determined by integration of thebenzylic proton signals in ¹H NMR spectrum. FIG. 15 shows the secondorder constant of compounds 61-68. A surprising finding was thatcompound 62, which does not have a hydroxyl function, reactsapproximately 70-times slower that the analogous 4-dibenzocyclooctynol(61). Acylation of the hydroxyl of 61 such as in compounds 63 and 64,led to a slow reduction in reaction rate. Alkylation of 61, as incompound 65, also resulted in a slower rate of reaction. Compound 66,which has a gem-difluoride reacted at a similar rate as compound 61.Interestingly, ketone 67 reacts with a slightly higher reaction ratethan 1. Oxime 68 has a similar reaction than 61. These resultsdemonstrate that modification of the hydroxyl of 61 can have a dramaticinfluence on the rate of cycloaddition.

Experimental

Synthesis of 70. To a stirring solution of LiAlH₄ (0.38 g, 10 mmol) andAlCl₃ (1.3 g, 10 mmol) in Et₂O (100 mL) was added 69 (1.1 g, 5 mmol).The reaction was kept at 0° C. for 12 hours, and then it was quenchedwith water (100 ml). The aqueous layer was extracted with ether (4×100ml), and the combined organic extracts were washed with water (100 ml)and brine (100 ml). The crude product was purified by columnchromatography (hexane/CH₂Cl₂, 2/1, v/v) to yield two 70 (0.63 g, 61%;Scheme 7; FIG. 16). ¹H NMR (CDCl₃, 300 MHz) δ: 6.90-7.21 (m, 8H,aromatics), 6.67 (s, 2H, CH═CH), 3.11 (s, 4H, —CH₂—CH2-). ¹³C NMR (75MHz, CDCl₃) δ: 140.0, 136.9, 131.6, 130.3, 130.1, 128.7, 128.5, 127.1,125.6. HRMS calcd for C₁₆H₁₄Na (M+Na): 229.0993. Found: 229.1003.

Synthesis of 71. A solution of bromine (0.4 g, 2.5 mmol) in CHCl₃ (10mL) was added dropwise to a solution of 70 (0.5 g, 2.5 mmol) in CHCl₃(20 mL) at 0° C. The reaction mixture was stirred at room temperaturefor 12 hours until the reaction was complete (monitored by TLC). Theresulting mixture was washed with aqueous saturated sodium thiosulfatesolution (15 mL), and dried (MgSO₄). The solvents were evaporated underreduced pressure and the residue was purified by silica gel columnchromatography (hexane/CH₂Cl₂, 10/1, v/v) to afford 71 (0.53 g, 58%;Scheme 7; FIG. 16). ¹H NMR (CDCl₃,300 MHz) δ: 7.06-7.52 (m, 8H,aromatics), 5.79 (s, 2H, Ph-CH—Br), 3.05 (dd, 2H, PhHCH), 2.84 (m, 2H,PhHCH). ¹³C NMR (75 MHz, CDCl₃) δ: 141.8, 138.7, 131.3, 130.6, 129.3,126.6, 35.7.

Synthesis of 62. To a solution of 71 (0.36 g, 1 mmol) in tetrahydrofuran(20 mL) was added dropwise t-BuOK in tetrahydrofuran (2.0 M), (2 mL)under an atmosphere of Argon at room temperature. The reaction mixturewas stirred for 2 hours at room temperature, after which it was pouredinto ice water (10 mL) and the resulting mixture was extracted withCH₂Cl₂ (2×50 mL). The combined extracts were washed with water, brineand dried (MgSO₄) and the solvents were evaporated under reducedpressure. The residue was purified by silica gel column chromatography(hexane/CH₂Cl₂, 2/1, v/v) to afford 62 (50 mg, 25%; Scheme 7; FIG. 16).¹H NMR (CDCl₃, 300 MHz) δ: 7.29-7.14 (m, 8H, aromatics), 3.28-3.15 (m,2H, —HCH—HCH—), 2.40-2.27 (m, 2H, —HCH—HCH—). ¹³C NMR (75 MHz, CDCl₃) δ:153.8, 129.6, 127.9, 126.7, 126.3, 124.2, 111.8, 36.7.

Synthesis of 63. To a stirring solution of 72 (38 mg, 0.1 mmol) inCH₂Cl₂ (15 mL) was added 73 (15 mg, 0.2 mmol) and TEA (10 μL). Thereaction mixture was stirred at room temperature for 12 hours. Thesolvents were evaporated under reduced pressure and the residue waspurified by silica gel column chromatography (CH₂Cl₂/CH₃OH, 20/1, v/v)to afford 63 (25 mg, 77%; Scheme 8; FIG. 17). ¹H NMR (CDCl₃, 300 MHz) δ:6.94-7.43 (m, 8H, aromatics), 5.42 (m, 1H, Ph-CH—O), 3.61 (m, 2H,CH₇OH), 3.30 (m, 2H, CH₂NH), 3.08 (dd, 1H, J=15.0, 1.8 Hz, PhHCH), 2.84(dd, 1H, J=15.0, 3.9 Hz, PhHCH), 1.53-1.68 (m, 2H, CH₂CH₂OH). ¹³C NMR(75 MHz, CDCl₃) δ: 150.8, 149.1, 128.9, 128.0, 127.0, 126.1, 126.0,125.9, 125.8, 125.3, 125.1, 125.0, 122.8, 122.6, 120.3, 111.9, 108.9,58.6, 45.2, 36.8, 36.7, 31.6. HRMS calcd for C₂₀H₁₉O₃Na (M+Na):344.1263. Found: 344.1896.

Synthesis of 64. To a stirring solution of 61 (22 mg, 0.1 mmol) inpyridine (4 mL) was added Ac₂O (1 mL). The reaction mixture was stirredat room temperature for 12 hours. The solvents were evaporated underreduced pressure and the residue was purified by silica gel columnchromatography (hexane/CH₂Cl₂, 1/1, v/v) to afford 64 (21 mg, 81%;Scheme 9; FIG. 18). ¹H NMR (CDCl₃, 300 MHz) δ: 7.43-7.17 (m, 8H,aromatics), 5.49 (m, 1H, Ph-CH—OAc), 3.06 (dd, 1H, J=15.6, 2.4 Hz,PhHCH), 2.84 (dd, 1H, J=15.6, 2.4 Hz, PhHCH), 2.17 (s, 3H, CH₃). ¹³C NMR(75 MHz, CDCl₃) δ: 169.9, 151.3, 151.1, 130.1, 128.3, 128.1, 127.4,127.3, 126.5, 126.2, 124.0, 121.6, 113.2, 110.0, 76.6, 46.5, 21.4. HRMScalcd for C₁₈H₁₄O₂Na (M+Na): 285.0891. Found: 285.1005.

Synthesis of 65. To a stirring solution of 61 (22 mg, 0.1 mmol) in DMF(2 mL) was added NaH (8 mg, 0.2 mmol), the mixture was stirred at roomtemperature for 1 hour and then benzyl bromide (BnBr, 34 mg, 0.2 mmol)was added. The reaction mixture was stirred at room temperature for 12hours. The solvents were evaporated under reduced pressure and theresidue was purified by silica gel column chromatography (hexane/CH₂Cl₂,2/1, v/v) to afford 65 (18 mg, 59%; Scheme 9; FIG. 18). ¹H NMR (CDCl₃,300 MHz) δ: 7.70 (m, 1H, aromatics), 7.39-7.17 (m, 13H, aromatics), 4.55(dd, 2H, J=11.6, 3.0 Hz, CH₂Ph), 4.26 (m, 1H, Ph-CH—OBn), 3.23 (dd, 1H,J=15.0, 2.4 Hz, PhHCH), 2.84 (dd, 1H, J=15.0, 2.4 Hz, PhHCH). ¹³C NMR(75 MHz, CDCl₃) δ: 152.6, 151.1, 137.3, 128.4, 127.3, 127.1, 127.0,126.5, 126.2, 125.8, 125.7, 125.1, 125.0, 123.6, 123.0, 120.5, 111.8,109.5, 81.5, 71.0, 46.1. HRMS calcd for C₂₃H₁₈ONa (M+Na): 333.1255.Found: 333.1905.

Synthesis of 74. To a stirring solution of LDA (20 ml, 40 mmol, 2.0 Msolution in THF) in THF (200 mL) at room temperature was added asolution of ketone 69 (4.4 g, 20 mmol) in THF (40 mL) over 1 hour usinga syringe pump. After an additional 20 minutes of stirring at roomtemperature, chlorotriethylsilane (6.7 ml, 40 mmol) was added. Thesolution was stirred at room temperature for 1 hour. The reactionmixture was concentrated on a rotary evaporator, and the crude productwas purified directly by column chromatography (hexane/CH₂Cl₂, 10/1,v/v) to yield a clear oil 74 (5.8 g, 85%; Scheme 10; FIG. 19). ¹H NMR(CDCl₃, 300 MHz) δ:7.25-6.95 (m, 8H, aromatics), 6.72 (t, 2H, J=7.0 Hz,CH═CH), 6.11 (s, 1H, J=7.0 Hz, CH═C), 0.87-0.82 (m, 9H, CH₂—CH₃),0.61-0.48 (m, 6H, CH₂—CH₃). ¹³C NMR (75 MHz, CDCl₃) δ: 151.9, 138.2,137.3, 137.2, 136.7, 136.5, 134.0, 132.6, 130.1, 129.3, 129.0, 128.6,128.0, 127.1, 127.0, 126.2, 112.7, 6.9, 5.1. HRMS calcd for C₂₂H₂₆OSiNa(M+Na): 357.1651. Found: 357.1993.

Synthesis of 75. To a stifling solution of fluorinating reagent(1-chloromethyl-4-fluoro-1,4-diazoniabicyclo[2.2.2]octanebis-(tetrafluoroborate)) available under the trade designationSELECTFLUOR from Air Products (Allentown, Pa.) (6.3. g, 18 mmol) in DMF(20 ml) at 0° C. was added a solution of silyl enol ether 74 (5.0 g, 15mmol) DMF (20 ml) via an addition funnel over 10 minutes. The reactionwas allowed to slowly warm to room temperature while stirring over 30minutes, and then it was quenched with water (100 mL). The aqueous layerwas extracted with ether (4×100 ml), and the combined organic extractswere washed with water (3×100 mL) and brine (1×200 mL). The crudeproduct was purified by column chromatography (hexane/CH₂Cl₂, 1/1, v/v)to yield 75 (2.4 g, 66%; Scheme 10; FIG. 19). ¹H NMR (CDCl₃, 300 MHz) δ:7.80-7.06 (m, 8H, aromatics), 6.85 (s, 2H, CH═CH), 4.41-4.36 (m,1H,CHF). ¹³C NMR (75 MHz, CDCl₃) δ: 196.4, 152.8, 144.1, 140.4, 138.5,135.8, 135.5, 135.4, 131.5, 129.6, 128.3, 127.7, 126.9, 125.3, 124.6,124.1, 63.6, 56.9; ¹⁹F(CDCl₃, 283 MHz) δ: −109.1 (s, 1F). HRMS calcd forC₁₆H₁₁FONa (M+Na): 261.0692. Found: 261.1237.

Synthesis of 76. To a stirring solution of LDA (10 ml, 20 mmol, 2.0 Msolution in THF) in THF (100 mL) at room temperature was added asolution of ketone 75 (2.4 g, 10 mmol) in THF (20 mL) over 1 hour usinga syringe pump. After an additional 20 minutes of stirring at roomtemperature, chlorotriethylsilane (3.3 ml, 20 mmol) was added. Thesolution was stirred at room temperature for 1 hour. The reactionmixture was concentrated on a rotary evaporator, and the crude productwas purified directly by column chromatography (hexane/CH₂Cl₂, 5/1, v/v)to yield a clear oil 76 (2.8 g, 79%; Scheme 10; FIG. 19). ¹H NMR (CDCl₃,300 MHz) δ:7.41 (m, 2H, aromatics), 7.22 (m, 4H, aromatics), 7.08 (m,2H, aromatics), 6.91 (s, 2H, CH═CH), 0.94 (t, 9H, J=7.8 Hz, CH₂—CH₃),0.63 (m, 6H, CH)—CH₃). ¹³C NMR (75 MHz, CDCl₃) δ: 145.8, 142.6, 137.3,137.2, 136.3, 136.1, 134.2, 133.3, 132.6, 132.1, 130.1, 130.0, 129.6,129.3, 128.9, 128.8, 128.7, 128.5, 128.2, 127.5, 127.4, 6.7, 6.3, 5.2;¹⁹F(CDCl₃, 283 MHz) δ:-111.978 (s, 1F). HRMS calcd for C₂₂H₂₃FOSiNa(M+Na): 373.1400. Found: 373.1522.

Synthesis of 77. To a stirring solution of SELECTFLUOR fluorinatingreagent (3.5. g, 10 mmol) in DMF (15 ml) at 0° C. was added a solutionof silyl enol ether 76 (2.8 g, 8 mmol) DMF (10 ml) via an additionfunnel over 10 minutes. The reaction was allowed to slowly warm to roomtemperature while stirring over 30 minutes, and then it was quenchedwith water (100 mL). The aqueous layer was extracted with ether (4×100mL), and the combined organic extracts were washed with water (3×100 mL)and brine (1×100 mL). The crude product was purified by columnchromatography (CH₂Cl₂) to yield 77 (1.0 g, 51%; Scheme 10; FIG. 19). ¹HNMR (CDCl₃, 300 MHz) δ: 8.05 (m, 1H, aromatics), 7.69 (m, 1H,aromatics), 7.51 (m, 1H, aromatics), 7.39-7.21 (m, 5H, aromatics), 6.92(d, 1H, CH═CH, J=14.8 Hz), 6.73 (d, 1H, CH═CH, J=14.8 Hz). ¹³C NMR (75MHz, CDCl₃) δ: 188.1, 134.6, 133.6, 132.8, 132.3, 131.1, 130.8, 130.5,130.1, 129.8, 129.6, 129.3, 126.8, 15.0, 124.8, 115.3; ¹⁹F(CDCl₃, 283MHz) δ: —110.1 (s, 2F). HRMS calcd for C₁₆H₁₀F₂ONa (M+Na): 279.0597.Found: 279.1032.

Synthesis of 78. To a stirring solution of 77 (1.0 g, 4 mmol) in EtOH(30 mL) was added NaBH₄ (0.3 g, 8 mmol) over 5 minutes. The reaction waskept at room temperature for 2 hours, and then it was quenched withwater (100 ml). The aqueous layer was extracted with CH₂Cl₂ (3×100 mL),and the combined organic extracts were washed with water (100 mL) andbrine (100 mL). The crude product was purified by column chromatography(hexane/EtOAc, 5/1, v/v) to yield 78 (0.78 g, 78%; Scheme 10; FIG. 19).¹H NMR (CDCl₃, 300 MHz) δ: 7.02-7.74 (m, 8H, aromatics), 6.94 (d, 1H,J=12.3 Hz, CH═CH), 6.85 (d, 1H, J=12.3 Hz, CH═CH), 5.60 (m, 1H,Ph-CH—OH), 2.82 (m, 1H, OH). ¹³C NMR (75 MHz, CDCl₃) δ: 136.0, 135.9,135.0, 133.8, 131.2, 130.6, 130.0, 128.1, 127.9, 126.8, 124.6, 121.5,121.4; ¹⁹F(CDCl₃, 282 MHz) δ: —69.8 (d, 1F, J=259.4 Hz), -111.7 (dd, 1F,J=259.4, 21.4 Hz). HRMS calcd for C₁₆H₁₂F₂ONa (M+Na): 281.0754. Found:281.1122.

Synthesis of 79. To a stirring solution of bromine (0.16 g, 1.0 mmol) inCHCl₃ (10 mL) was added dropwise to a solution of 78 (0.25 g, 1.0 mmol)in CHCl₃ (10 mL) at 0° C. The reaction mixture was stirred at roomtemperature for 12 hours until the reaction was complete (monitored byTLC). The resulting mixture was washed with aqueous saturated sodiumthiosulfate solution (10 mL), and dried (MgSO₄). The solvents wereevaporated under reduced pressure and the residue was purified by silicagel column chromatography (hexane/EtOAc, 8/1, v/v) to afford 79 (0.19 g,46%; Scheme 10; FIG. 19). ¹H NMR (CDCl₃, 300 MHz) δ: 6.96-7.82 (m, 8H,aromatics), 5.62 (d, 1H, J=10.8 Hz, Ph-CH—Br), 5.17 (d, 1H, J=10.8 Hz,PhHCH). ¹³C NMR (75 MHz, CDCl₃) δ: 132.7, 132.4, 131.0, 130.8, 129.2,129.0, 128, 128.4, 128.3, 127.8, 125.4, 123.8, 111.5, 57.3, 56.5, 50.5;¹⁹F(CDCl₃, 282 MHz) δ: —98.8 (d, 1F, J=341.1 Hz), -110.4 (d, 1F, J=341.1Hz).

Synthesis of 66. To a stirring solution of 79 (40 mg, 0.1 mmol) intetrahydrofuran (10 mL) was added dropwise t-BuOK in tetrahydrofuran(2.0 M), (0.5 mL) under an atmosphere of Argon at room temperature. Thereaction mixture was stirred for 6 hours at room temperature, afterwhich it was poured into ice water (10 mL) and the resulting mixture wasextracted with CH₂Cl₂ (2×50 mL). The combined extracts were washed withwater, brine and dried (MgSO₄) and the solvents were evaporated underreduced pressure. The residue was purified by silica gel columnchromatography (hexane/EtOAc, 5/1, v/v) to afford 66 (10 mg, 49%; Scheme10; FIG. 19). ¹H NMR (CDCl₃, 300 MHz) δ: 7.19-7.92 (m, 8H, aromatics),5.39 (d, 1H, J=23.4, 10.8 Hz, —CH—OH). ¹³C NMR (75 MHz, CDCl₃) δ: 131.3,129.5, 129.4, 128.4, 127.9, 127.5, 126.8, 126.6, 125.9, 125.7, 124.8,124.5, 120.3, 107.3, 82.8; ¹⁹F(CDCl₃, 282 MHz) 6: —91.5 (d, 1F, J=253.8Hz).-103.4 (d, 1F, 1=253.8 Hz).

(6H-11,12-didehydro-dibenzo [a,e]cycloocten-5-ylideneaminooxy)-aceticacid (68). A solution of6H-11,12-didehydro-dibenzo[a,e]cyclooctatrien-5-one 67 (21.8 mg, 0.1mmol) and carboxymethyl)hydroxylamine hemihydrochloride (21.8 mg, 0.2mmol) in 1:1:0.02 v/v/v MeOH/CH₂Cl₂/HOAc (8 ml) was stirred at roomtemperature for 2 days. The solvent was removed under reduced pressure,and the residue was purified by flash chromatography on silica gel(EtOAc) to give the product as white solid (17.8 mg, 61%). ¹H NMR (300MHz, CDCl₃): δ 7.54 (1H, d, J=7.4 Hz), 7.46 (1H, d, J=7.4 Hz), 7.18-7.39(6H, m), 4.53 (2H, m), 4.23 (1H, d, J=12.8 Hz), 3.16 (1H, d, J=12.8 Hz).¹³C NMR (75 MHz, CDCl₃): δ 175.2 & 173.6, 154.1 153.2, 130.7, 129.5,19.3, 129.2, 129.1, 128.1, 128.0, 127.1, 126.9, 125.5, 125.2, 122.7,113.9, 111.2, 84.7, 68.3 & 67.1, 35.0 & 33.2. MALDI HRMS: m/z 314.0810[M+Na⁺]. Calcd for C₁₈H₁₃NNaO₃: 314.0793.

Modification of Macromolecules and Nano-Material Using Cycloadditionswith 4-dibenzocyclooctynol

The Cu(I) catalyzed 1,3-dipolar cycloaddition of azides with terminalalkynes to give stable triazoles has been employed for tagging a varietyof biomolecules including proteins, nucleic acids, lipids, andsaccharides. This reaction has also been used to modify polymers andnanoscale materials. Potential difficulties to remove Cu(I), which ishighly cytotoxic, complicates the use of the 1,3-dipolar cycloadditionfor conjugation of compounds or material for biological or medicalapplication. The use of 4-dibenzocyclooctynol instead of a terminalalkyne for cycloadditions with azides should overcome this problem.

To demonstrate the use of 4-dibenzocyclooctynol in bioconjugation,co-block polymers 83 and 84 were prepared. These materials were employedto form organomicelles in water and it was shown that4-dibenzocyclooctyne fragment of these materials can be reacted was withazido containing molecules (FIGS. 20A, B).

It is well known that co-block polymers composed of a polyester andpolyethyleneglycol fragment self-assemble in water to formorganomicelles. These nano-materials have attracted attention as drugdelivery devises. Derivatization of organomicelles with, for example,tissue or tumor targeting moieties may lead to smart drug deliverydevises. In addition, modification of organomicelles with fluorescenttags or MRI reagents, such as biotin, will be valuable for imagingpurposes (FIG. 20C).

Copolymerization of polyethylene glycol methyl ether (81) or azide (82)(MW ˜2000 Da) with caprolactone in the presence of a catalytic amount ofSnOct gave copolymers 83 and 84, respectively (Scheme 11; FIG. 21). Theazido fragment of 84 was reduced with triphenylphosphine and the amineof the resulting polymer 85 was reacted with 86 and 87 to givedibenzocyclooctyl derivatives 88 and 89, respectively. A mixture of 83and 88 or 89 (9/1, w/w) dissolved in a small amount of THF were added towater. Cryo-TEM showed that organomicelles that have a diameter ofapproximately 40A were formed. The resulting micelles were incubatedwith azido-containing saccharide 90 and after a reaction time of 24hours, unreacted saccharide was removed by dialysis. The micelles wereanalyzed for sugar content by hydrolysis with TFA followed byquantification by high pH anion exchange chromatography. It wasestablished that approximately 45% of the cyclooctynes were modified bysaccharides.

It is to be expected that compound 84 can also be employed for theformation of micelles and the azido moieties of the resulting azidesemployed in cycloaddition with compounds modified with adibenzocyclooctyl fragment.

Experimental

Synthesis of PEG₄₄-b-PCL₂₆ 83. PEG₄₅-b-PCL₂₃ block copolymers weresynthesized as reported. A predetermined volume (12.0 mL) ofε-caprolactone monomer was placed in a flask containing an amount (9.0g) of PEG 81 under an argon atmosphere. Then, a drop of SnOct was added.After cooling to liquid-nitrogen temperature, the flask was evacuatedfor 12 hours, sealed off, and kept at 130° C. for 24 hours. Thesynthesized polymers were dissolved in THF, recovered by precipitationby cold hexane, and dried under vacuum at room temperature. The degreeof polymerization of the PCL was calculated by ¹H NMR relative to thedegree of polymerization of the PEG 81.

Synthesis of azide-PEG₄₄-b-PCL₂₆ 84. Azide-PEG-b-PCL was synthesized bya one-pot cationic ring opening polymerization at 130° C. under a streamof argon adopting a previously reported method for the preparation ofPEG-b-PCL with some modifications. Briefly, a predetermined volume (3.3mL) of ε-caprolactone monomer was placed in a flask containing apreweighed amount (2.5 g) of azide-PEG-OH 82 under a nitrogenatmosphere. Then a drop of SnOct was added. After cooling toliquid-nitrogen temperature, the flask was evacuated, sealed off, andkept at 130° C. for 24 hours. The synthesized polymers were thendissolved in THF, recovered by precipitation into cold hexane, and driedunder vacuum at room temperature. The number average molecular weight(M_(n)) of azide-PEO₄₄-b-PCL₂₆ ₈4 block copolymer was determined by ¹HNMR.

Synthesis of amine-PEG₄₄-b-PCL₂₆ 85. Pd/C (10 wt. % on activated carbon,50 mg) was added to a solution of azide-PEG₄₄-b-PCL₂₆ 84 (200 mg) inEtOH and HOAc (50 μL) after which H₂ was bubbled through the solutionfor 1 hr followed by stirring under an H₂ atmosphere for 16 hours. Themixture was filtered, concentrated in vacuum. The residues were thendissolved in THF, recovered by precipitation into cold hexane, and driedunder vacuum at room temperature to afford amine-PEG₄₄-b-PCL₇₆ 85.

DIDO-PEO-PCL copolymer (88). To a stirred solution of carbonic acid5,6-dihydro-11,12-didehydro-dibenzo[a,e]cycloocten-5-yl ester4-nitro-phenyl ester 86 (11.6 mg, 0.03 mmol) and copolymer 85 (98 mg,0.02 mmol) in CH₂Cl₂ (10 ml) at room temperature was added Et₃N (0.014ml, 0.1 mmol). The reaction mixture was stirred overnight at roomtemperature, after which the solvent was removed under reduced pressure.The residue was purified by size exclusion chromatography (SEC) on LH-20column (1:1 v/v MeOH/CH₂Cl₂) to give the product as yellowish solid (101mg, 97%).

DIDO-PEO-PCL copolymer (89). To a stirred solution of(5,6-Dihydro-11,12-didehydro-dibenzo[a,e]cycloocten-5-yloxy)-acetic acid88 (8.3 mg, 0.03 mmol) and copolymer 85 (98 mg, 0.02 mmol) in DMF (15ml) at room temperature was added HATU coupling reagent (11.4 mg, 0.03mmol) and DIPEA (0.0104 ml, 0.06 mmol). The reaction mixture was stirredfor 5 hours at room temperature, after which the solvent was removedunder reduced pressure. The residue was purified by SEC chromatographyon LH-20 column (1:1 v/v MeOH/CF₂Cl₂) to give the product as yellowishsolid (100 mg, 96%).

Cycloadditions of dibenzocyclooctanol with various 1,3-dipoles.

It has been found that 4-dibenzocyclooctynol can react in the absence ofcatalyst or promoter at ambient temperature with 1,3-dipoles such asnitrones and acyl diazo derivatives, which can provide uniqueopportunities for bioconjugation reactions.

Nitrones were prepared by a modification of the procedures disclosed inDicken et al., J. Org. Chem. 1982, 47, 2047-2051; and Inouye et al.,Bull. Chem. Soc. Jpn. 1983, 56, 3541-3542. N-alkylhydroxylaminehydrochloride (10.0 mmol), glyoxylic acid (0.92 g, 10.0 mmol), andsodium bicarbonate (1.68 g, 20.0 mmol) in toluene (20 ml) were stirredat room temperature overnight. The solid was filtered and the filtratewas concentrated to afford the nitrone. This nitrone was then useddirectly without any purification.

Thus nitrones 91-95 were mixed with 4-dibenzocyclooctynol and after areaction time of 3 minutes to 3.5 hours the corresponding2,3-dihydro-issoxazole cycloaddition products were isolated in almost aquantitative yield. It can be seen in FIG. 18 that the chemical natureof the nitrone has a dramatic impact of the reaction rate. In particularelectron poor nitrones 93 and 94 react at much faster rates thancorresponding azides.

Experimental

General method for calculating second order rate constants by NMR.Substrates were dissolved separately in the appropriate solvent andmixed 1:1 at 6 mM concentrations. Percent conversion was monitored bothby disappearance of starting material and appearance of the tworegioisomeric products as determined by integration at multiple chemicalshifts. Second order rate constants for the reaction were determined byplotting the 1/[substrates] versus time and analysis by linearregression. Second order rate constants correspond to one half of thedetermined slope.

The complete disclosure of all patents, patent applications, andpublications, and electronically available material (e.g., GenBank aminoacid and nucleotide sequence submissions; and protein data bank (pdb)submissions) cited herein are incorporated by reference. The foregoingdetailed description and examples have been given for clarity ofunderstanding only. No unnecessary limitations are to be understoodtherefrom. The invention is not limited to the exact details shown anddescribed, for variations obvious to one skilled in the art will beincluded within the invention defined by the claims.

1. An alkyne of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═N—OR³, C═N—NR₃R₄,CHOR³, or CHNHR³; and each R³ and R⁴ independently represents hydrogenor an organic group. 2-3. (canceled)
 4. The alkyne claim 1 wherein R³comprises a covalently bound organic dye.
 5. (canceled)
 6. The alkyne ofclaim 1 wherein X represents C═N—OR³ and R³ represents an organic grouphaving the formula —(CH₂)_(a)C(O)Y, wherein: a is 1-3; Y represents OHor NHR⁵; and R⁵ represents hydrogen or a biotinylation product of aprimary amine-containing organic group.
 7. The alkyne of claim 6 whereinthe biotinylation product is the biotinylation product of a primaryamine-containing group of the formula —(CH₂CH₂O)_(b)(CH₂)_(c)-L_(d)(CH₂CH₂O)_(e)(CH₂)_(f)NH₂ and/or—(CD₂CD₂O)_(b)-L_(d)-(CD₂CD₂O)_(e)(CD₂)_(f)NH₂, wherein b=0 to 100; c=0to 100; d=0 to 100; e=0 to 100; f=0 to 100; and L is an optionalcleavable linker.
 8. The alkyne of claim 7 wherein the cleavable linker,if present, is a disulfide.
 9. The alkyne of claim 1 wherein Xrepresents CHOR³ and R³ is selected from the group consisting of analkyl group, an aryl group, an alkaryl group, and an aralkyl group. 10.The alkyne of claim 9 wherein R³ represents —C(O)Z, wherein: Zrepresents an alkyl group, OR⁶, or NHR⁷; R⁶ and R⁷ are eachindependently selected from the group consisting of an alkyl group, anaryl group, an alkaryl group, and an aralkyl group.
 11. The alkyne ofclaim 10 wherein R⁷ is a biotinylation product of a primaryamine-containing organic group.
 12. The alkyne of claim 11 wherein thebiotinylation product is the biotinylation product of a primaryamine-containing group of the formula —(CH₂CH₂O)_(b)(CH₂)_(c)-L_(d)-(CH₂CH₂O)_(e)(CH₂)_(f)NH₂ and/or—(CD₂CD₂O)_(b)(CD₂)_(c)-L_(d)-(CD₂CD₂O)_(e)(CD₂)_(f)NH₂, wherein b=0 to100; c=0 to 100; d=0 to 100; e=0 to 100; f=0 to 100; and L is anoptional cleavable linker.
 13. The alkyne of claim 12 wherein thecleavable linker, if present, is a disulfide.
 14. The alkyne claim 1wherein R³ represents a polymeric or a copolymeric group.
 15. The alkyneof claim 14 wherein the copolymeric group comprises a hydrophilicsegment and a hydrophobic segment.
 16. The alkyne of claim 14 whereinthe copolymeric group comprises a fragment of the formula—[CH₂CH₂O]_(n)—[C(O)(CH₂)]_(m)—H, wherein n=0 to 100 and m=0 to
 100. 17.An alkyne of the formula:


18. An alkyne of the formula:


19. An alkyne of the formula:


20. An alkyne of the formula:

wherein R³ represents hydrogen or an organic group.
 21. A compositioncomprising a blend of: an alkyne according to claim 14; and a polymer ora copolymer. 22-24. (canceled)
 25. The composition of claim 21 whereinthe composition forms a copolymer micelle.
 26. A method for controllingthe delivery of drugs, the method comprising: combining at least one1,3-dipole-functional drug with a copolymer micelle according to claim25 comprising an alkyne; and allowing the at least one1,3-dipole-functional drug and the copolymer micelle comprising thealkyne to react under conditions effective to form a heterocycliccompound.
 27. A compound of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; each R³ and R⁴ independently representshydrogen or an organic group; and R⁸ represents an organic group.
 28. Acompound of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═N—OR³, C═N—NR³R⁴,CHOR³, or CHNHR³; each R³ and R⁴ independently represents hydrogen or anorganic group; and R⁸ represents an organic group. 29-30. (canceled) 31.A compound of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C1-C10 organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNHR³; and each R³, R⁴, and R¹⁰ independentlyrepresents hydrogen or an organic group, with the proviso that at leastone R¹⁰ represents an organic group.
 32. A compound of the formula:

wherein: each R¹ is independently selected from the group consisting ofhydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite, sulfate, and aC1-C10 organic group; each R² is independently selected from the groupconsisting of hydrogen, halogen, hydroxy, alkoxy, nitrate, nitrite,sulfate, and a C₁-C₁₀ organic group; X represents C═O, C═N—OR³,C═N—NR³R⁴, CHOR³, or CHNTHR³; and each R³, R⁴, and R¹⁰ independentlyrepresents hydrogen or an organic group, with the proviso that at leastone R¹⁰ represents an organic group. 33-34. (canceled)
 35. A method ofpreparing a heterocyclic compound, the method comprising: combining atleast one 1,3-dipole-functional compound with at least one alkyneaccording to claim 1; and allowing the at least one1,3-dipole-functional compound and the at least one alkyne to reactunder conditions effective to form the heterocyclic compound. 36-59.(canceled)
 60. A substrate having on the surface thereof an alkyneaccording to claim
 1. 61-63. (canceled)
 64. A method of immobilizing abiomolecule on a substrate, the method comprising: providing a substrateaccording claim 60; contacting the substrate with a1,3-dipole-functional biomolecule under conditions effective to form aheterocyclic compound. 65-68. (canceled)
 69. A method for immobilizing acell, the method comprising: providing a substrate according to claim60; contacting the substrate with a cell comprising a1,3-dipole-functional biomolecule under conditions effective to form aheterocyclic compound.